") },
+ { assert path(process.out.log.get(0).get(1)).getText().contains("total bases: 13683") },
{ assert snapshot(
+ process.out.json,
process.out.reads,
process.out.reads_fail,
- process.out.json,
- process.out.versions).match() },
- { assert process.out.reads_merged == [] },
- { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") },
- { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") },
+ process.out.reads_merged,
+ process.out.versions).match() }
)
}
}
- test("test_fastp_paired_end_trim_fail") {
+ test("test_fastp_single_end_qc_only") {
- config './nextflow.save_failed.config'
when {
process {
"""
input[0] = Channel.of([
- [ id:'test', single_end:false ], // meta map
- [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+ [ id:'test', single_end:true ],
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
])
input[1] = []
- input[2] = false
- input[3] = true
+ input[2] = true
+ input[3] = false
input[4] = false
"""
}
@@ -253,19 +265,22 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
+ { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") },
+ { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") },
{ assert snapshot(
+ process.out.json,
+ process.out.reads,
process.out.reads,
process.out.reads_fail,
- process.out.json,
- process.out.versions).match() },
- { assert process.out.reads_merged == [] },
- { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 162") },
- { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") }
+ process.out.reads_fail,
+ process.out.reads_merged,
+ process.out.reads_merged,
+ process.out.versions).match() }
)
}
}
- test("test_fastp_paired_end_merged") {
+ test("test_fastp_paired_end_qc_only") {
when {
process {
@@ -276,9 +291,9 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
])
input[1] = []
- input[2] = false
+ input[2] = true
input[3] = false
- input[4] = true
+ input[4] = false
"""
}
}
@@ -286,34 +301,37 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
+ { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") },
+ { assert path(process.out.log.get(0).get(1)).getText().contains("Q30 bases: 12281(88.3716%)") },
{ assert snapshot(
+ process.out.json,
process.out.reads,
+ process.out.reads,
+ process.out.reads_fail,
+ process.out.reads_fail,
process.out.reads_merged,
- process.out.json,
- process.out.versions).match() },
- { assert process.out.reads_fail == [] },
- { assert path(process.out.log.get(0).get(1)).getText().contains("total reads: 75") },
- { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") }
+ process.out.reads_merged,
+ process.out.versions).match() }
)
}
}
- test("test_fastp_paired_end_merged-stub") {
+ test("test_fastp_single_end - stub") {
- options '-stub'
+ options "-stub"
when {
+
process {
"""
input[0] = Channel.of([
- [ id:'test', single_end:false ], // meta map
- [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+ [ id:'test', single_end:true ],
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
])
input[1] = []
input[2] = false
input[3] = false
- input[4] = true
+ input[4] = false
"""
}
}
@@ -321,25 +339,33 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(process.out).match() },
+ { assert snapshot(process.out).match() }
)
}
}
- test("test_fastp_paired_end_merged_adapterlist") {
+ test("test_fastp_paired_end - stub") {
+
+ options "-stub"
when {
+
process {
"""
+ adapter_fasta = []
+ save_trimmed_pass = true
+ save_trimmed_fail = false
+ save_merged = false
+
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
])
- input[1] = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ])
+ input[1] = []
input[2] = false
input[3] = false
- input[4] = true
+ input[4] = false
"""
}
}
@@ -347,29 +373,25 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(
- process.out.reads,
- process.out.reads_merged,
- process.out.json,
- process.out.versions).match() },
- { assert process.out.reads_fail == [] },
- { assert path(process.out.log.get(0).get(1)).getText().contains("total bases: 13683") },
- { assert path(process.out.html.get(0).get(1)).getText().contains("
") }
+ { assert snapshot(process.out).match() }
)
}
}
- test("test_fastp_single_end_qc_only") {
+ test("fastp - stub test_fastp_interleaved") {
+
+ options "-stub"
+ config './nextflow.interleaved.config'
when {
process {
"""
input[0] = Channel.of([
- [ id:'test', single_end:true ],
- [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+ [ id:'test', single_end:true ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ]
])
input[1] = []
- input[2] = true
+ input[2] = false
input[3] = false
input[4] = false
"""
@@ -379,55 +401,101 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(
- process.out.reads,
- process.out.reads_fail,
- process.out.reads_merged,
- process.out.json,
- process.out.versions).match() },
- { assert process.out.reads == [] },
- { assert process.out.reads_fail == [] },
- { assert process.out.reads_merged == [] },
- { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") },
- { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") },
+ { assert snapshot(process.out).match() }
)
}
}
- test("test_fastp_single_end_qc_only-stub") {
+ test("test_fastp_single_end_trim_fail - stub") {
- options '-stub'
+ options "-stub"
when {
+
process {
"""
input[0] = Channel.of([
- [ id:'test', single_end:true ],
+ [ id:'test', single_end:true ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
])
input[1] = []
- input[2] = true
- input[3] = false
+ input[2] = false
+ input[3] = true
input[4] = false
"""
}
}
then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test_fastp_paired_end_trim_fail - stub") {
+ options "-stub"
+
+ config './nextflow.save_failed.config'
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+ ])
+ input[1] = []
+ input[2] = false
+ input[3] = true
+ input[4] = false
+ """
+ }
+ }
+
+ then {
assertAll(
{ assert process.success },
- { assert snapshot(process.out).match() },
+ { assert snapshot(process.out).match() }
)
}
}
- test("test_fastp_paired_end_qc_only") {
+ test("test_fastp_paired_end_merged - stub") {
+
+ options "-stub"
when {
- params {
- outdir = "$outputDir"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+ ])
+ input[1] = []
+ input[2] = false
+ input[3] = false
+ input[4] = true
+ """
}
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test_fastp_paired_end_merged_adapterlist - stub") {
+
+ options "-stub"
+
+ when {
process {
"""
input[0] = Channel.of([
@@ -435,6 +503,33 @@ nextflow_process {
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
])
+ input[1] = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ])
+ input[2] = false
+ input[3] = false
+ input[4] = true
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test_fastp_single_end_qc_only - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:true ],
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+ ])
input[1] = []
input[2] = true
input[3] = false
@@ -446,24 +541,14 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(
- process.out.reads,
- process.out.reads_merged,
- process.out.reads_fail,
- process.out.json,
- process.out.versions).match() },
- { assert process.out.reads == [] },
- { assert process.out.reads_fail == [] },
- { assert process.out.reads_merged == [] },
- { assert path(process.out.log.get(0).get(1)).getText().contains("Q30 bases: 12281(88.3716%)") },
- { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") },
+ { assert snapshot(process.out).match() }
)
}
}
- test("test_fastp_paired_end_qc_only-stub") {
+ test("test_fastp_paired_end_qc_only - stub") {
- options '-stub'
+ options "-stub"
when {
process {
@@ -484,7 +569,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(process.out).match() },
+ { assert snapshot(process.out).match() }
)
}
}
diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap
index b609b9a2..54be7e45 100644
--- a/modules/nf-core/fastp/tests/main.nf.test.snap
+++ b/modules/nf-core/fastp/tests/main.nf.test.snap
@@ -1,24 +1,15 @@
{
- "test_fastp_paired_end_qc_only-stub": {
+ "test_fastp_single_end_qc_only - stub": {
"content": [
{
"0": [
- [
- {
- "id": "test",
- "single_end": false
- },
- [
- "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
- "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
- ]
- ]
+
],
"1": [
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -27,7 +18,7 @@
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -36,7 +27,7 @@
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -54,7 +45,7 @@
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -63,7 +54,7 @@
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -72,22 +63,13 @@
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"reads": [
- [
- {
- "id": "test",
- "single_end": false
- },
- [
- "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
- "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
- ]
- ]
+
],
"reads_fail": [
@@ -104,10 +86,19 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-08T05:42:26.603745039"
+ "timestamp": "2024-07-05T14:31:10.841098"
},
"test_fastp_paired_end": {
"content": [
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
+ ]
+ ],
[
[
{
@@ -119,6 +110,48 @@
"test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
]
]
+ ],
+ [
+
+ ],
+ [
+
+ ],
+ [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-05T13:43:28.665779"
+ },
+ "test_fastp_paired_end_merged_adapterlist": {
+ "content": [
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.json:md5,5914ca3f21ce162123a824e33e8564f6"
+ ]
+ ],
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672",
+ "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba"
+ ]
+ ]
+ ],
+ [
+
],
[
[
@@ -126,7 +159,95 @@
"id": "test",
"single_end": false
},
- "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
+ "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5"
+ ]
+ ],
+ [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-05T13:44:18.210375"
+ },
+ "test_fastp_single_end_qc_only": {
+ "content": [
+ [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.json:md5,5cc5f01e449309e0e689ed6f51a2294a"
+ ]
+ ],
+ [
+
+ ],
+ [
+
+ ],
+ [
+
+ ],
+ [
+
+ ],
+ [
+
+ ],
+ [
+
+ ],
+ [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-05T13:44:27.380974"
+ },
+ "test_fastp_paired_end_trim_fail": {
+ "content": [
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test_1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7",
+ "test_2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a"
+ ]
+ ]
+ ],
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.paired.fail.fastq.gz:md5,409b687c734cedd7a1fec14d316e1366",
+ "test_1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6",
+ "test_2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995"
+ ]
+ ]
+ ],
+ [
+
+ ],
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519"
]
],
[
@@ -137,9 +258,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T13:02:09.747686552"
+ "timestamp": "2024-07-05T13:43:58.749589"
},
- "fastp test_fastp_interleaved - stub": {
+ "fastp - stub test_fastp_interleaved": {
"content": [
{
"0": [
@@ -238,97 +359,248 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T13:03:09.374379128"
+ "timestamp": "2024-07-05T13:50:00.270029"
},
- "test_fastp_paired_end_merged_adapterlist": {
+ "test_fastp_single_end - stub": {
"content": [
- [
- [
- {
- "id": "test",
- "single_end": false
- },
+ {
+ "0": [
[
- "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672",
- "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba"
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "4": [
+
+ ],
+ "5": [
+
+ ],
+ "6": [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+ ],
+ "html": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "json": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "log": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "reads": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ],
+ "reads_fail": [
+
+ ],
+ "reads_merged": [
+
+ ],
+ "versions": [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
]
- ],
- [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5"
- ]
- ],
- [
- [
- {
- "id": "test",
- "single_end": false
- },
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- "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
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+ }
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"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T13:04:47.637461379"
+ "timestamp": "2024-07-05T13:49:42.502789"
},
- "test_fastp_single_end_qc_only": {
+ "test_fastp_paired_end_merged_adapterlist - stub": {
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- [
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+ "single_end": false
+ },
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+ "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
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+ "single_end": false
+ },
+ "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
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+ [
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+ "id": "test",
+ "single_end": false
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+ "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
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+ "3": [
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+ "single_end": false
+ },
+ "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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+ ],
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+ [
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+ "single_end": false
+ },
+ "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ],
+ "6": [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+ ],
+ "html": [
+ [
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+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
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+ "json": [
+ [
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+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
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+ "log": [
+ [
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+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
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+ "reads": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
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+ "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
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+ ],
+ "reads_fail": [
+
+ ],
+ "reads_merged": [
+ [
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+ "id": "test",
+ "single_end": false
+ },
+ "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
]
- ],
- [
- "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
- ]
+ }
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T20:11:50.885505279"
+ "timestamp": "2024-07-05T13:54:53.458252"
},
- "test_fastp_single_end-stub": {
+ "test_fastp_paired_end_merged - stub": {
"content": [
{
"0": [
[
{
"id": "test",
- "single_end": true
+ "single_end": false
},
- "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ [
+ "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
]
],
"1": [
[
{
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- "single_end": true
+ "single_end": false
},
"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
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@@ -337,7 +609,7 @@
[
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- "single_end": true
+ "single_end": false
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"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
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@@ -346,7 +618,7 @@
[
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+ "single_end": false
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -355,7 +627,13 @@
],
"5": [
-
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
],
"6": [
"versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
@@ -364,7 +642,7 @@
[
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- "single_end": true
+ "single_end": false
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -373,7 +651,7 @@
[
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+ "single_end": false
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"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -382,7 +660,7 @@
[
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- "single_end": true
+ "single_end": false
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -391,16 +669,25 @@
[
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- "single_end": true
+ "single_end": false
},
- "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ [
+ "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
]
],
"reads_fail": [
],
"reads_merged": [
-
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
],
"versions": [
"versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
@@ -411,9 +698,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T13:01:55.987280865"
+ "timestamp": "2024-07-05T13:50:27.689379"
},
- "test_fastp_paired_end_trim_fail": {
+ "test_fastp_paired_end_merged": {
"content": [
[
[
@@ -421,10 +708,7 @@
"id": "test",
"single_end": false
},
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- "test_1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7",
- "test_2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a"
- ]
+ "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc"
]
],
[
@@ -434,11 +718,13 @@
"single_end": false
},
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- "test_1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6",
- "test_2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995"
+ "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672",
+ "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba"
]
]
+ ],
+ [
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],
[
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@@ -446,7 +732,7 @@
"id": "test",
"single_end": false
},
- "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519"
+ "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5"
]
],
[
@@ -457,7 +743,7 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T13:03:46.458766801"
+ "timestamp": "2024-07-05T13:44:08.68476"
},
"test_fastp_paired_end - stub": {
"content": [
@@ -564,52 +850,19 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-08T05:36:36.446112695"
+ "timestamp": "2024-07-05T13:49:51.679221"
},
- "test_fastp_paired_end_merged": {
+ "test_fastp_single_end": {
"content": [
[
[
{
"id": "test",
- "single_end": false
- },
- [
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- "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba"
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- "single_end": false
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- "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5"
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- ],
- [
- [
- {
- "id": "test",
- "single_end": false
+ "single_end": true
},
- "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc"
+ "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc"
]
],
- [
- "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
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- ],
- "meta": {
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- "nextflow": "24.04.2"
- },
- "timestamp": "2024-06-10T13:04:09.964580373"
- },
- "test_fastp_single_end": {
- "content": [
[
[
{
@@ -620,13 +873,10 @@
]
],
[
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- "id": "test",
- "single_end": true
- },
- "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc"
- ]
+
+ ],
+ [
+
],
[
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@@ -636,28 +886,25 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T13:01:34.044931225"
+ "timestamp": "2024-07-05T13:43:18.834322"
},
- "test_fastp_paired_end_merged-stub": {
+ "test_fastp_single_end_trim_fail - stub": {
"content": [
{
"0": [
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
- [
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- "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
- ]
+ "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
[
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- "single_end": false
+ "single_end": true
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"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
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@@ -666,7 +913,7 @@
[
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+ "single_end": true
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -675,22 +922,22 @@
[
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+ "single_end": true
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"4": [
-
- ],
- "5": [
[
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- "single_end": false
+ "single_end": true
},
- "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ "test.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
+ ],
+ "5": [
+
],
"6": [
"versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
@@ -699,7 +946,7 @@
[
{
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- "single_end": false
+ "single_end": true
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -708,7 +955,7 @@
[
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+ "single_end": true
},
"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -717,7 +964,7 @@
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -726,25 +973,22 @@
[
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"id": "test",
- "single_end": false
+ "single_end": true
},
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- "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
- "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
- ]
+ "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"reads_fail": [
-
- ],
- "reads_merged": [
[
{
"id": "test",
- "single_end": false
+ "single_end": true
},
- "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ "test.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
+ ],
+ "reads_merged": [
+
],
"versions": [
"versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
@@ -755,16 +999,16 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-08T05:39:42.022707162"
+ "timestamp": "2024-07-05T14:05:36.898142"
},
- "test_fastp_single_end_qc_only-stub": {
+ "test_fastp_paired_end_trim_fail - stub": {
"content": [
{
"0": [
[
{
"id": "test",
- "single_end": true
+ "single_end": false
},
[
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@@ -776,7 +1020,7 @@
[
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- "single_end": true
+ "single_end": false
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"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -785,7 +1029,7 @@
[
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"id": "test",
- "single_end": true
+ "single_end": false
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -794,13 +1038,23 @@
[
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+ "single_end": false
},
"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"4": [
-
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ]
],
"5": [
@@ -812,7 +1066,7 @@
[
{
"id": "test",
- "single_end": true
+ "single_end": false
},
"test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
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@@ -821,7 +1075,7 @@
[
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+ "single_end": false
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"test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
@@ -830,7 +1084,7 @@
[
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+ "single_end": false
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"test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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@@ -839,7 +1093,7 @@
[
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+ "single_end": false
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[
"test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
@@ -848,7 +1102,17 @@
]
],
"reads_fail": [
-
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ]
],
"reads_merged": [
@@ -862,7 +1126,7 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T13:05:31.722431847"
+ "timestamp": "2024-07-05T14:05:49.212847"
},
"fastp test_fastp_interleaved": {
"content": [
@@ -892,7 +1156,7 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-07T22:35:04.608948751"
+ "timestamp": "2024-07-05T13:43:38.910832"
},
"test_fastp_single_end_trim_fail": {
"content": [
@@ -902,7 +1166,7 @@
"id": "test",
"single_end": true
},
- "test.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7"
+ "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5"
]
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[
@@ -911,7 +1175,7 @@
"id": "test",
"single_end": true
},
- "test.fail.fastq.gz:md5,3e4aaadb66a5b8fc9b881bf39c227abd"
+ "test.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7"
]
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[
@@ -920,8 +1184,11 @@
"id": "test",
"single_end": true
},
- "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5"
+ "test.fail.fastq.gz:md5,3e4aaadb66a5b8fc9b881bf39c227abd"
]
+ ],
+ [
+
],
[
"versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
@@ -931,10 +1198,19 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T13:03:23.130471376"
+ "timestamp": "2024-07-05T13:43:48.22378"
},
"test_fastp_paired_end_qc_only": {
"content": [
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.json:md5,623064a45912dac6f2b64e3f2e9901df"
+ ]
+ ],
[
],
@@ -945,13 +1221,13 @@
],
[
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- "single_end": false
- },
- "test.fastp.json:md5,623064a45912dac6f2b64e3f2e9901df"
- ]
+
+ ],
+ [
+
+ ],
+ [
+
],
[
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@@ -961,6 +1237,95 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-10T20:12:14.00927619"
+ "timestamp": "2024-07-05T13:44:36.334938"
+ },
+ "test_fastp_paired_end_qc_only - stub": {
+ "content": [
+ {
+ "0": [
+
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "4": [
+
+ ],
+ "5": [
+
+ ],
+ "6": [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+ ],
+ "html": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "json": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "log": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "reads": [
+
+ ],
+ "reads_fail": [
+
+ ],
+ "reads_merged": [
+
+ ],
+ "versions": [
+ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-05T14:31:27.096468"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c86..d8989f48 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
def rename_to = old_new_pairs*.join(' ').join(' ')
def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
- def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+ // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+ // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+ // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+ def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
// FastQC memory value allowed range (100 - 10000)
def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 70edae4d..e9d79a07 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -23,17 +23,14 @@ nextflow_process {
then {
assertAll (
- { assert process.success },
-
- // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
- // looks like this:
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-
- { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
- { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
- { assert path(process.out.html[0][1]).text.contains("
| File type | Conventional base calls |
") },
-
- { assert snapshot(process.out.versions).match("fastqc_versions_single") }
+ { assert process.success },
+ // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+ // looks like this:
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+ { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+ { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+ { assert path(process.out.html[0][1]).text.contains("| File type | Conventional base calls |
") },
+ { assert snapshot(process.out.versions).match() }
)
}
}
@@ -54,16 +51,14 @@ nextflow_process {
then {
assertAll (
- { assert process.success },
-
- { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
- { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
- { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
- { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
- { assert path(process.out.html[0][1][0]).text.contains("| File type | Conventional base calls |
") },
- { assert path(process.out.html[0][1][1]).text.contains("| File type | Conventional base calls |
") },
-
- { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
+ { assert process.success },
+ { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+ { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+ { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+ { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+ { assert path(process.out.html[0][1][0]).text.contains("| File type | Conventional base calls |
") },
+ { assert path(process.out.html[0][1][1]).text.contains("| File type | Conventional base calls |
") },
+ { assert snapshot(process.out.versions).match() }
)
}
}
@@ -83,13 +78,11 @@ nextflow_process {
then {
assertAll (
- { assert process.success },
-
- { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
- { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
- { assert path(process.out.html[0][1]).text.contains("| File type | Conventional base calls |
") },
-
- { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
+ { assert process.success },
+ { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+ { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+ { assert path(process.out.html[0][1]).text.contains("| File type | Conventional base calls |
") },
+ { assert snapshot(process.out.versions).match() }
)
}
}
@@ -109,13 +102,11 @@ nextflow_process {
then {
assertAll (
- { assert process.success },
-
- { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
- { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
- { assert path(process.out.html[0][1]).text.contains("| File type | Conventional base calls |
") },
-
- { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
+ { assert process.success },
+ { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+ { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+ { assert path(process.out.html[0][1]).text.contains("| File type | Conventional base calls |
") },
+ { assert snapshot(process.out.versions).match() }
)
}
}
@@ -138,22 +129,20 @@ nextflow_process {
then {
assertAll (
- { assert process.success },
-
- { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
- { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
- { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
- { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
- { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
- { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
- { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
- { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
- { assert path(process.out.html[0][1][0]).text.contains("| File type | Conventional base calls |
") },
- { assert path(process.out.html[0][1][1]).text.contains("| File type | Conventional base calls |
") },
- { assert path(process.out.html[0][1][2]).text.contains("| File type | Conventional base calls |
") },
- { assert path(process.out.html[0][1][3]).text.contains("| File type | Conventional base calls |
") },
-
- { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
+ { assert process.success },
+ { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+ { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+ { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+ { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+ { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+ { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+ { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+ { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+ { assert path(process.out.html[0][1][0]).text.contains("| File type | Conventional base calls |
") },
+ { assert path(process.out.html[0][1][1]).text.contains("| File type | Conventional base calls |
") },
+ { assert path(process.out.html[0][1][2]).text.contains("| File type | Conventional base calls |
") },
+ { assert path(process.out.html[0][1][3]).text.contains("| File type | Conventional base calls |
") },
+ { assert snapshot(process.out.versions).match() }
)
}
}
@@ -173,21 +162,18 @@ nextflow_process {
then {
assertAll (
- { assert process.success },
-
- { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
- { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
- { assert path(process.out.html[0][1]).text.contains("| File type | Conventional base calls |
") },
-
- { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
+ { assert process.success },
+ { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+ { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+ { assert path(process.out.html[0][1]).text.contains("| File type | Conventional base calls |
") },
+ { assert snapshot(process.out.versions).match() }
)
}
}
test("sarscov2 single-end [fastq] - stub") {
- options "-stub"
-
+ options "-stub"
when {
process {
"""
@@ -201,12 +187,123 @@ nextflow_process {
then {
assertAll (
- { assert process.success },
- { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
- process.out.zip.collect { file(it[1]).getName() } +
- process.out.versions ).match("fastqc_stub") }
+ { assert process.success },
+ { assert snapshot(process.out).match() }
)
}
}
+ test("sarscov2 paired-end [fastq] - stub") {
+
+ options "-stub"
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [id: 'test', single_end: false], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("sarscov2 interleaved [fastq] - stub") {
+
+ options "-stub"
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [id: 'test', single_end: false], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("sarscov2 paired-end [bam] - stub") {
+
+ options "-stub"
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [id: 'test', single_end: false], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("sarscov2 multiple [fastq] - stub") {
+
+ options "-stub"
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [id: 'test', single_end: false], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("sarscov2 custom_prefix - stub") {
+
+ options "-stub"
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'mysample', single_end:true ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
}
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 86f7c311..d5db3092 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,88 +1,392 @@
{
- "fastqc_versions_interleaved": {
+ "sarscov2 custom_prefix": {
"content": [
[
"versions.yml:md5,e1cc25ca8af856014824abd842e93978"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-01-31T17:40:07.293713"
+ "timestamp": "2024-07-22T11:02:16.374038"
},
- "fastqc_stub": {
+ "sarscov2 single-end [fastq] - stub": {
"content": [
- [
- "test.html",
- "test.zip",
- "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
- ]
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "html": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "zip": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T11:02:24.993809"
+ },
+ "sarscov2 custom_prefix - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "mysample",
+ "single_end": true
+ },
+ "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "mysample",
+ "single_end": true
+ },
+ "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "html": [
+ [
+ {
+ "id": "mysample",
+ "single_end": true
+ },
+ "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "zip": [
+ [
+ {
+ "id": "mysample",
+ "single_end": true
+ },
+ "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ }
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-01-31T17:31:01.425198"
+ "timestamp": "2024-07-22T11:03:10.93942"
},
- "fastqc_versions_multiple": {
+ "sarscov2 interleaved [fastq]": {
"content": [
[
"versions.yml:md5,e1cc25ca8af856014824abd842e93978"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-01-31T17:40:55.797907"
+ "timestamp": "2024-07-22T11:01:42.355718"
},
- "fastqc_versions_bam": {
+ "sarscov2 paired-end [bam]": {
"content": [
[
"versions.yml:md5,e1cc25ca8af856014824abd842e93978"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-01-31T17:40:26.795862"
+ "timestamp": "2024-07-22T11:01:53.276274"
},
- "fastqc_versions_single": {
+ "sarscov2 multiple [fastq]": {
"content": [
[
"versions.yml:md5,e1cc25ca8af856014824abd842e93978"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-01-31T17:39:27.043675"
+ "timestamp": "2024-07-22T11:02:05.527626"
},
- "fastqc_versions_paired": {
+ "sarscov2 paired-end [fastq]": {
"content": [
[
"versions.yml:md5,e1cc25ca8af856014824abd842e93978"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T11:01:31.188871"
+ },
+ "sarscov2 paired-end [fastq] - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "html": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "zip": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T11:02:34.273566"
+ },
+ "sarscov2 multiple [fastq] - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "html": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "zip": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-01-31T17:39:47.584191"
+ "timestamp": "2024-07-22T11:03:02.304411"
},
- "fastqc_versions_custom_prefix": {
+ "sarscov2 single-end [fastq]": {
"content": [
[
"versions.yml:md5,e1cc25ca8af856014824abd842e93978"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T11:01:19.095607"
+ },
+ "sarscov2 interleaved [fastq] - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "html": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "zip": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T11:02:44.640184"
+ },
+ "sarscov2 paired-end [bam] - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "html": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+ ],
+ "zip": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-01-31T17:41:14.576531"
+ "timestamp": "2024-07-22T11:02:53.550742"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test
index a124bff5..18d35f49 100644
--- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test
+++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test
@@ -17,14 +17,14 @@ nextflow_process {
"""
input[0] = [
[ id:'test_bam' ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
[],
[]
]
- input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
- input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]
- input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ]
+ input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+ input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ]
input[4] = [ [], [] ]
input[5] = [ [], [] ]
@@ -35,9 +35,12 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- // { assert snapshot(process.out).match() }, // Unstable hashes
- { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_bam_input") },
- { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_bam_input") },
+ { assert snapshot(
+ file(process.out.vcf[0][1]).name,
+ file(process.out.tbi[0][1]).name,
+ process.out.versions
+ ).match()
+ }
)
}
@@ -50,14 +53,14 @@ nextflow_process {
"""
input[0] = [
[ id:'test_cram' ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[],
[]
]
- input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
- input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]
- input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ]
+ input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+ input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ]
input[4] = [ [], [] ]
input[5] = [ [], [] ]
"""
@@ -67,9 +70,12 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- // { assert snapshot(process.out).match() }, // Unstable hashes
- { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input") },
- { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input") },
+ { assert snapshot(
+ file(process.out.vcf[0][1]).name,
+ file(process.out.tbi[0][1]).name,
+ process.out.versions
+ ).match()
+ }
)
}
@@ -82,16 +88,16 @@ nextflow_process {
"""
input[0] = [
[ id:'test_cram_sites' ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[],
[]
]
- input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
- input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]
- input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ]
- input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ]
- input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ]
+ input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+ input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ]
+ input[4] = [ [ id:'test_sites' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) ]
+ input[5] = [ [ id:'test_sites_tbi' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) ]
"""
}
}
@@ -99,9 +105,12 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- // { assert snapshot(process.out).match() }, // Unstable hashes
- { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input_with_sites") },
- { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input_with_sites") },
+ { assert snapshot(
+ file(process.out.vcf[0][1]).name,
+ file(process.out.tbi[0][1]).name,
+ process.out.versions
+ ).match()
+ }
)
}
@@ -114,16 +123,16 @@ nextflow_process {
"""
input[0] = [
[ id:'test_cram_sites_dragstr' ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[],
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true)
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt', checkIfExists: true)
]
- input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
- input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]
- input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ]
- input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ]
- input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ]
+ input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+ input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ]
+ input[4] = [ [ id:'test_sites' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) ]
+ input[5] = [ [ id:'test_sites_tbi' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) ]
"""
}
}
@@ -131,9 +140,12 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- // { assert snapshot(process.out).match() }, // Unstable hashes
- { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_dragstr_input_with_sites") },
- { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_dragstr_input_with_sites") },
+ { assert snapshot(
+ file(process.out.vcf[0][1]).name,
+ file(process.out.tbi[0][1]).name,
+ process.out.versions
+ ).match()
+ }
)
}
diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap
index 375025ee..0203fcfc 100644
--- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap
@@ -1,82 +1,58 @@
{
- "gatk_hc_vcf_cram_dragstr_input_with_sites": {
+ "homo_sapiens - [cram, crai] - fasta - fai - dict": {
"content": [
- "test_cram_sites_dragstr.vcf.gz"
+ "test_cram.vcf.gz",
+ "test_cram.vcf.gz.tbi",
+ [
+ "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab"
+ ]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-02-20T13:24:45.142682"
+ "timestamp": "2024-08-14T09:36:54.158605"
},
- "gatk_hc_vcf_bam_input": {
+ "homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi": {
"content": [
- "test_bam.vcf.gz"
+ "test_cram_sites.vcf.gz",
+ "test_cram_sites.vcf.gz.tbi",
+ [
+ "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab"
+ ]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-02-20T13:23:19.203837"
+ "timestamp": "2024-08-14T09:37:13.77024"
},
- "gatk_hc_vcf_cram_input": {
+ "homo_sapiens - [bam, bai] - fasta - fai - dict": {
"content": [
- "test_cram.vcf.gz"
+ "test_bam.vcf.gz",
+ "test_bam.vcf.gz.tbi",
+ [
+ "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab"
+ ]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-02-20T13:23:48.434615"
+ "timestamp": "2024-08-14T09:36:34.77631"
},
- "gatk_hc_vcf_cram_input_with_sites": {
+ "homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi": {
"content": [
- "test_cram_sites.vcf.gz"
+ "test_cram_sites_dragstr.vcf.gz",
+ "test_cram_sites_dragstr.vcf.gz.tbi",
+ [
+ "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab"
+ ]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-02-20T13:24:17.147745"
- },
- "gatk_hc_vcf_tbi_bam_input": {
- "content": [
- "test_bam.vcf.gz.tbi"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
- },
- "timestamp": "2024-02-20T13:23:19.23048"
- },
- "gatk_hc_vcf_tbi_cram_input": {
- "content": [
- "test_cram.vcf.gz.tbi"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
- },
- "timestamp": "2024-02-20T13:23:48.45958"
- },
- "gatk_hc_vcf_tbi_cram_dragstr_input_with_sites": {
- "content": [
- "test_cram_sites_dragstr.vcf.gz.tbi"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
- },
- "timestamp": "2024-02-20T13:24:45.154818"
- },
- "gatk_hc_vcf_tbi_cram_input_with_sites": {
- "content": [
- "test_cram_sites.vcf.gz.tbi"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
- },
- "timestamp": "2024-02-20T13:24:17.158138"
+ "timestamp": "2024-08-14T09:37:32.967085"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test
index b4910126..7a5eee09 100644
--- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test
+++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test
@@ -14,10 +14,10 @@ nextflow_process {
when {
process {
"""
- input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), []]
- input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
- input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
- input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
+ input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), []]
+ input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+ input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
+ input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ]
"""
}
}
@@ -25,7 +25,11 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads") }
+ { assert snapshot(
+ file(process.out.bam[0][1]).name,
+ process.out.versions
+ ).match()
+ }
)
}
@@ -36,10 +40,10 @@ nextflow_process {
when {
process {
"""
- input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
- input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
- input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
- input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
+ input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)]
+ input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+ input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
+ input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ]
"""
}
}
@@ -47,7 +51,11 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_intervals") }
+ { assert snapshot(
+ file(process.out.bam[0][1]).name,
+ process.out.versions
+ ).match()
+ }
)
}
@@ -60,10 +68,10 @@ nextflow_process {
when {
process {
"""
- input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), [], []]
- input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
- input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
- input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
+ input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [], []]
+ input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+ input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
+ input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ]
"""
}
}
@@ -71,7 +79,11 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_stub") }
+ { assert snapshot(
+ file(process.out.bam[0][1]).name,
+ process.out.versions
+ ).match()
+ }
)
}
diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap
index 3e581ceb..5a348453 100644
--- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap
@@ -1,32 +1,41 @@
{
"test_gatk4_splitncigarreads_intervals": {
"content": [
- "test.bam"
+ "test.bam",
+ [
+ "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb"
+ ]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-02-15T08:26:10.91960579"
+ "timestamp": "2024-08-16T12:29:41.948726"
},
"test_gatk4_splitncigarreads_stub": {
"content": [
- "test.bam"
+ "test.bam",
+ [
+ "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb"
+ ]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-02-15T08:26:32.322712467"
+ "timestamp": "2024-08-16T12:29:53.2252"
},
"test_gatk4_splitncigarreads": {
"content": [
- "test.bam"
+ "test.bam",
+ [
+ "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb"
+ ]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-02-15T08:25:53.532205456"
+ "timestamp": "2024-08-16T12:29:30.774423"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
index 25910b34..dfc02a7b 100644
--- a/modules/nf-core/gunzip/environment.yml
+++ b/modules/nf-core/gunzip/environment.yml
@@ -4,4 +4,6 @@ channels:
- bioconda
- defaults
dependencies:
- - conda-forge::sed=4.7
+ - conda-forge::grep=3.11
+ - conda-forge::sed=4.8
+ - conda-forge::tar=1.34
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
index 468a6f28..5e67e3b9 100644
--- a/modules/nf-core/gunzip/main.nf
+++ b/modules/nf-core/gunzip/main.nf
@@ -4,8 +4,8 @@ process GUNZIP {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'nf-core/ubuntu:20.04' }"
+ 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
+ 'nf-core/ubuntu:22.04' }"
input:
tuple val(meta), path(archive)
@@ -18,8 +18,11 @@ process GUNZIP {
task.ext.when == null || task.ext.when
script:
- def args = task.ext.args ?: ''
- gunzip = archive.toString() - '.gz'
+ def args = task.ext.args ?: ''
+ def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1]
+ def name = archive.toString() - '.gz' - ".$extension"
+ def prefix = task.ext.prefix ?: name
+ gunzip = prefix + ".$extension"
"""
# Not calling gunzip itself because it creates files
# with the original group ownership rather than the
@@ -37,7 +40,11 @@ process GUNZIP {
"""
stub:
- gunzip = archive.toString() - '.gz'
+ def args = task.ext.args ?: ''
+ def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1]
+ def name = archive.toString() - '.gz' - ".$extension"
+ def prefix = task.ext.prefix ?: name
+ gunzip = prefix + ".$extension"
"""
touch $gunzip
cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
index 231034f2..f32973a0 100644
--- a/modules/nf-core/gunzip/meta.yml
+++ b/modules/nf-core/gunzip/meta.yml
@@ -37,3 +37,4 @@ maintainers:
- "@joseespinosa"
- "@drpatelh"
- "@jfy133"
+ - "@gallvp"
diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test
index 6406008e..776211ad 100644
--- a/modules/nf-core/gunzip/tests/main.nf.test
+++ b/modules/nf-core/gunzip/tests/main.nf.test
@@ -33,4 +33,89 @@ nextflow_process {
}
+ test("Should run without failures - prefix") {
+
+ config './nextflow.config'
+
+ when {
+ params {
+ outdir = "$outputDir"
+ }
+ process {
+ """
+ input[0] = Channel.of([
+ [ id: 'test' ],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+ ]
+ )
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
+ test("Should run without failures - stub") {
+
+ options '-stub'
+
+ when {
+ params {
+ outdir = "$outputDir"
+ }
+ process {
+ """
+ input[0] = Channel.of([
+ [],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+ ]
+ )
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
+ test("Should run without failures - prefix - stub") {
+
+ options '-stub'
+ config './nextflow.config'
+
+ when {
+ params {
+ outdir = "$outputDir"
+ }
+ process {
+ """
+ input[0] = Channel.of([
+ [ id: 'test' ],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+ ]
+ )
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
}
diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap
index 720fd9ff..069967e7 100644
--- a/modules/nf-core/gunzip/tests/main.nf.test.snap
+++ b/modules/nf-core/gunzip/tests/main.nf.test.snap
@@ -1,4 +1,70 @@
{
+ "Should run without failures - prefix - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+ ],
+ "gunzip": [
+ [
+ {
+ "id": "test"
+ },
+ "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-06-25T11:35:10.861293"
+ },
+ "Should run without failures - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ [
+
+ ],
+ "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+ ],
+ "gunzip": [
+ [
+ [
+
+ ],
+ "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-06-25T11:35:05.857145"
+ },
"Should run without failures": {
"content": [
{
@@ -26,6 +92,43 @@
]
}
],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
"timestamp": "2023-10-17T15:35:37.690477896"
+ },
+ "Should run without failures - prefix": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+ ],
+ "gunzip": [
+ [
+ {
+ "id": "test"
+ },
+ "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-06-25T11:33:32.921739"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config
new file mode 100644
index 00000000..dec77642
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: GUNZIP {
+ ext.prefix = { "${meta.id}.xyz" }
+ }
+}
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ecb7dd7b..a31464c9 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::multiqc=1.22.3
+ - bioconda::multiqc=1.24.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 2581a496..d5365800 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.22.3--pyhdfd78af_0' :
- 'biocontainers/multiqc:1.22.3--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' :
+ 'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
input:
path multiqc_files, stageAs: "?/*"
path(multiqc_config)
path(extra_multiqc_config)
path(multiqc_logo)
+ path(replace_names)
+ path(sample_names)
output:
path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
script:
def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
def config = multiqc_config ? "--config $multiqc_config" : ''
def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+ def replace = replace_names ? "--replace-names ${replace_names}" : ''
+ def samples = sample_names ? "--sample-names ${sample_names}" : ''
"""
multiqc \\
--force \\
$args \\
$config \\
+ $prefix \\
$extra_config \\
$logo \\
+ $replace \\
+ $samples \\
.
cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 45a9bc35..382c08cb 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -29,6 +29,19 @@ input:
type: file
description: Optional logo file for MultiQC
pattern: "*.{png}"
+ - replace_names:
+ type: file
+ description: |
+ Optional two-column sample renaming file. First column a set of
+ patterns, second column a set of corresponding replacements. Passed via
+ MultiQC's `--replace-names` option.
+ pattern: "*.{tsv}"
+ - sample_names:
+ type: file
+ description: |
+ Optional TSV file with headers, passed to the MultiQC --sample_names
+ argument.
+ pattern: "*.{tsv}"
output:
- report:
type: file
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index f1c4242e..33316a7d 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
tag "modules_nfcore"
tag "multiqc"
+ config "./nextflow.config"
+
test("sarscov2 single-end [fastqc]") {
when {
@@ -17,6 +19,8 @@ nextflow_process {
input[1] = []
input[2] = []
input[3] = []
+ input[4] = []
+ input[5] = []
"""
}
}
@@ -41,6 +45,8 @@ nextflow_process {
input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
input[2] = []
input[3] = []
+ input[4] = []
+ input[5] = []
"""
}
}
@@ -66,6 +72,8 @@ nextflow_process {
input[1] = []
input[2] = []
input[3] = []
+ input[4] = []
+ input[5] = []
"""
}
}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 0a4760e4..83fa080c 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
"multiqc_versions_single": {
"content": [
[
- "versions.yml:md5,bf3b209659477254bb8fa5a9405f9984"
+ "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-25T12:31:21.878452033"
+ "timestamp": "2024-07-10T12:41:34.562023"
},
"multiqc_stub": {
"content": [
@@ -17,25 +17,25 @@
"multiqc_report.html",
"multiqc_data",
"multiqc_plots",
- "versions.yml:md5,bf3b209659477254bb8fa5a9405f9984"
+ "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-25T12:32:02.322196503"
+ "timestamp": "2024-07-10T11:27:11.933869532"
},
"multiqc_versions_config": {
"content": [
[
- "versions.yml:md5,bf3b209659477254bb8fa5a9405f9984"
+ "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-25T12:31:50.064227638"
+ "timestamp": "2024-07-10T11:26:56.709849369"
}
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 00000000..c537a6a3
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: 'MULTIQC' {
+ ext.prefix = null
+ }
+}
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
index 73ba7dc6..87a8c7d8 100644
--- a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
+++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::picard=3.1.1
+ - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
index 06c4bc17..99153992 100644
--- a/modules/nf-core/picard/collectinsertsizemetrics/main.nf
+++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTINSERTSIZEMETRICS {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
- 'biocontainers/picard:3.1.1--hdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+ 'biocontainers/picard:3.2.0--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
index 542b2e82..1dfb9654 100644
--- a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
+++ b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
@@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- - bioconda::picard=3.1.1
+ - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
index f833a105..0c8f2cfa 100644
--- a/modules/nf-core/picard/collectrnaseqmetrics/main.nf
+++ b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTRNASEQMETRICS {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
- 'biocontainers/picard:3.1.1--hdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+ 'biocontainers/picard:3.2.0--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index b523c21b..e002585b 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -35,10 +35,11 @@ process SAMTOOLS_INDEX {
"""
stub:
+ def args = task.ext.args ?: ''
+ def extension = file(input).getExtension() == 'cram' ?
+ "crai" : args.contains("-c") ? "csi" : "bai"
"""
- touch ${input}.bai
- touch ${input}.crai
- touch ${input}.csi
+ touch ${input}.${extension}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test
index bb7756d1..ca34fb5c 100644
--- a/modules/nf-core/samtools/index/tests/main.nf.test
+++ b/modules/nf-core/samtools/index/tests/main.nf.test
@@ -9,11 +9,7 @@ nextflow_process {
tag "samtools/index"
test("bai") {
-
when {
- params {
- outdir = "$outputDir"
- }
process {
"""
input[0] = Channel.of([
@@ -27,18 +23,13 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out.bai).match("bai") },
- { assert snapshot(process.out.versions).match("bai_versions") }
+ { assert snapshot(process.out).match() }
)
}
}
test("crai") {
-
when {
- params {
- outdir = "$outputDir"
- }
process {
"""
input[0] = Channel.of([
@@ -52,20 +43,83 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out.crai).match("crai") },
- { assert snapshot(process.out.versions).match("crai_versions") }
+ { assert snapshot(process.out).match() }
)
}
}
test("csi") {
-
config "./csi.nextflow.config"
when {
- params {
- outdir = "$outputDir"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.csi[0][1]).name,
+ process.out.versions
+ ).match() }
+ )
+ }
+ }
+
+ test("bai - stub") {
+ options "-stub"
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("crai - stub") {
+ options "-stub"
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+ ])
+ """
}
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("csi - stub") {
+ options "-stub"
+ config "./csi.nextflow.config"
+
+ when {
process {
"""
input[0] = Channel.of([
@@ -79,8 +133,7 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert path(process.out.csi.get(0).get(1)).exists() },
- { assert snapshot(process.out.versions).match("csi_versions") }
+ { assert snapshot(process.out).match() }
)
}
}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap
index 52756e85..799d199c 100644
--- a/modules/nf-core/samtools/index/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap
@@ -1,74 +1,250 @@
{
- "crai_versions": {
+ "csi - stub": {
"content": [
- [
- "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
- ]
+ {
+ "0": [
+
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+
+ ],
+ "3": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ],
+ "bai": [
+
+ ],
+ "crai": [
+
+ ],
+ "csi": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ]
+ }
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-05-28T15:42:04.203740976"
+ "timestamp": "2024-07-22T16:51:53.9057"
},
- "csi_versions": {
+ "crai - stub": {
"content": [
- [
- "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
- ]
+ {
+ "0": [
+
+ ],
+ "1": [
+
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ],
+ "bai": [
+
+ ],
+ "crai": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "csi": [
+
+ ],
+ "versions": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ]
+ }
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-05-28T15:42:09.57475878"
+ "timestamp": "2024-07-22T16:51:45.931558"
},
- "crai": {
+ "bai - stub": {
"content": [
- [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+
+ ],
+ "2": [
+
+ ],
+ "3": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ],
+ "bai": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "crai": [
+
+ ],
+ "csi": [
+
+ ],
+ "versions": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
]
- ]
+ }
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-02-12T18:41:38.446424"
+ "timestamp": "2024-07-22T16:51:34.807525"
},
- "bai": {
+ "csi": {
"content": [
+ "test.paired_end.sorted.bam.csi",
[
- [
- {
- "id": "test",
- "single_end": false
- },
- "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
- ]
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-02-12T18:40:46.579747"
+ "timestamp": "2024-07-22T16:52:55.688799"
},
- "bai_versions": {
+ "crai": {
"content": [
- [
- "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
- ]
+ {
+ "0": [
+
+ ],
+ "1": [
+
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+ ]
+ ],
+ "3": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ],
+ "bai": [
+
+ ],
+ "crai": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+ ]
+ ],
+ "csi": [
+
+ ],
+ "versions": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T16:51:17.609533"
+ },
+ "bai": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+ ]
+ ],
+ "1": [
+
+ ],
+ "2": [
+
+ ],
+ "3": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ],
+ "bai": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+ ]
+ ],
+ "crai": [
+
+ ],
+ "csi": [
+
+ ],
+ "versions": [
+ "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+ ]
+ }
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-05-28T15:41:57.929287369"
+ "timestamp": "2024-07-22T16:51:04.16585"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
index 8e9c48b1..ae67e004 100644
--- a/modules/nf-core/star/align/main.nf
+++ b/modules/nf-core/star/align/main.nf
@@ -81,6 +81,8 @@ process STAR_ALIGN {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
+ echo "" | gzip > ${prefix}.unmapped_1.fastq.gz
+ echo "" | gzip > ${prefix}.unmapped_2.fastq.gz
touch ${prefix}Xd.out.bam
touch ${prefix}.Log.final.out
touch ${prefix}.Log.out
@@ -89,8 +91,6 @@ process STAR_ALIGN {
touch ${prefix}.toTranscriptome.out.bam
touch ${prefix}.Aligned.unsort.out.bam
touch ${prefix}.Aligned.sortedByCoord.out.bam
- touch ${prefix}.unmapped_1.fastq.gz
- touch ${prefix}.unmapped_2.fastq.gz
touch ${prefix}.tab
touch ${prefix}.SJ.out.tab
touch ${prefix}.ReadsPerGene.out.tab
diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test
index 6ecd7786..2d9f72dd 100644
--- a/modules/nf-core/star/align/tests/main.nf.test
+++ b/modules/nf-core/star/align/tests/main.nf.test
@@ -9,27 +9,367 @@ nextflow_process {
tag "star/align"
tag "star/genomegenerate"
- setup {
- run("STAR_GENOMEGENERATE") {
- script "../../../star/genomegenerate/main.nf"
+ test("homo_sapiens - single_end") {
+ config "./nextflow.config"
+
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
+ when {
process {
"""
input[0] = Channel.of([
- [ id:'test_fasta' ],
- [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ [ id:'test', single_end:true ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ]
])
- input[1] = Channel.of([
+ input[1] = STAR_GENOMEGENERATE.out.index
+ input[2] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
+ input[3] = false
+ input[4] = 'illumina'
+ input[5] = false
"""
}
}
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.log_final[0][1]).name,
+ file(process.out.log_out[0][1]).name,
+ file(process.out.log_progress[0][1]).name,
+ process.out.bam,
+ process.out.bam_sorted,
+ process.out.bam_transcript,
+ process.out.bam_unsorted,
+ process.out.bedgraph,
+ process.out.fastq,
+ process.out.junction,
+ process.out.read_per_gene_tab,
+ process.out.sam,
+ process.out.spl_junc_tab,
+ process.out.tab,
+ process.out.wig,
+ process.out.versions
+ ).match() }
+ )
+ }
}
- test("homo_sapiens - single_end") {
+ test("homo_sapiens - paired_end") {
+ config "./nextflow.config"
+
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+ ]
+ ])
+ input[1] = STAR_GENOMEGENERATE.out.index
+ input[2] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ input[3] = false
+ input[4] = 'illumina'
+ input[5] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.log_final[0][1]).name,
+ file(process.out.log_out[0][1]).name,
+ file(process.out.log_progress[0][1]).name,
+ process.out.bam,
+ process.out.bam_sorted,
+ process.out.bam_transcript,
+ process.out.bam_unsorted,
+ process.out.bedgraph,
+ process.out.fastq,
+ process.out.junction,
+ process.out.read_per_gene_tab,
+ process.out.sam,
+ process.out.spl_junc_tab,
+ process.out.tab,
+ process.out.wig,
+ process.out.versions
+ ).match() }
+ )
+ }
+ }
+
+ test("homo_sapiens - paired_end - arriba") {
+ config "./nextflow.arriba.config"
+
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+ ]
+ ])
+ input[1] = STAR_GENOMEGENERATE.out.index
+ input[2] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ input[3] = false
+ input[4] = 'illumina'
+ input[5] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.log_final[0][1]).name,
+ file(process.out.log_out[0][1]).name,
+ file(process.out.log_progress[0][1]).name,
+ process.out.bam,
+ process.out.bam_sorted,
+ process.out.bam_transcript,
+ process.out.bam_unsorted,
+ process.out.bedgraph,
+ process.out.fastq,
+ process.out.junction,
+ process.out.read_per_gene_tab,
+ process.out.sam,
+ process.out.spl_junc_tab,
+ process.out.tab,
+ process.out.wig,
+ process.out.versions
+ ).match() }
+ )
+ }
+ }
+
+ test("homo_sapiens - paired_end - starfusion") {
+ config "./nextflow.starfusion.config"
+
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+ ]
+ ])
+ input[1] = STAR_GENOMEGENERATE.out.index
+ input[2] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ input[3] = false
+ input[4] = 'illumina'
+ input[5] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.log_final[0][1]).name,
+ file(process.out.log_out[0][1]).name,
+ file(process.out.log_progress[0][1]).name,
+ process.out.bam,
+ process.out.bam_sorted,
+ process.out.bam_transcript,
+ process.out.bam_unsorted,
+ process.out.bedgraph,
+ process.out.fastq,
+ process.out.junction,
+ process.out.read_per_gene_tab,
+ process.out.sam,
+ process.out.spl_junc_tab,
+ process.out.tab,
+ process.out.wig,
+ process.out.versions
+ ).match() }
+ )
+ }
+ }
+
+ test("homo_sapiens - paired_end - multiple") {
config "./nextflow.config"
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+ ]
+ ])
+ input[1] = STAR_GENOMEGENERATE.out.index
+ input[2] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ input[3] = false
+ input[4] = 'illumina'
+ input[5] = false
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.log_final[0][1]).name,
+ file(process.out.log_out[0][1]).name,
+ file(process.out.log_progress[0][1]).name,
+ process.out.bam,
+ process.out.bam_sorted,
+ process.out.bam_transcript,
+ process.out.bam_unsorted,
+ process.out.bedgraph,
+ process.out.fastq,
+ process.out.junction,
+ process.out.read_per_gene_tab,
+ process.out.sam,
+ process.out.spl_junc_tab,
+ process.out.tab,
+ process.out.wig,
+ process.out.versions
+ ).match() }
+ )
+ }
+ }
+
+ test("homo_sapiens - single_end - stub") {
+ options "-stub"
+ config "./nextflow.config"
+
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
when {
process {
"""
@@ -52,29 +392,33 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - single_end - log_final") },
- { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - single_end - log_out") },
- { assert snapshot(process.out.bam).match("homo_sapiens - single_end - bam") },
- { assert snapshot(process.out.bam_sorted).match("homo_sapiens - single_end - bam_sorted") },
- { assert snapshot(process.out.bam_transcript).match("homo_sapiens - single_end - bam_transcript") },
- { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - single_end - bam_unsorted") },
- { assert snapshot(process.out.bedgraph).match("homo_sapiens - single_end - bedgraph") },
- { assert snapshot(process.out.fastq).match("homo_sapiens - single_end - fastq") },
- { assert snapshot(process.out.junction).match("homo_sapiens - single_end - junction") },
- { assert snapshot(process.out.log_progress).match("homo_sapiens - single_end - log_progress") },
- { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - single_end - read_per_gene_tab") },
- { assert snapshot(process.out.sam).match("homo_sapiens - single_end - sam") },
- { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - single_end - spl_junc_tab") },
- { assert snapshot(process.out.tab).match("homo_sapiens - single_end - tab") },
- { assert snapshot(process.out.wig).match("homo_sapiens - single_end - wig") },
- { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") }
+ { assert snapshot(process.out).match() }
)
}
}
- test("homo_sapiens - paired_end") {
+ test("homo_sapiens - paired_end - stub") {
+ options "-stub"
config "./nextflow.config"
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
when {
process {
"""
@@ -100,29 +444,33 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - log_final") },
- { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - log_out") },
- { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - bam") },
- { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - bam_sorted") },
- { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - bam_transcript") },
- { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - bam_unsorted") },
- { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - bedgraph") },
- { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - fastq") },
- { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - junction") },
- { assert snapshot(process.out.log_progress).match("homo_sapiens - paired_end - log_progress") },
- { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - read_per_gene_tab") },
- { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - sam") },
- { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - spl_junc_tab") },
- { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - tab") },
- { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - wig") },
- { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") }
+ { assert snapshot(process.out).match() }
)
}
}
- test("homo_sapiens - paired_end - arriba") {
+ test("homo_sapiens - paired_end - arriba - stub") {
+ options "-stub"
config "./nextflow.arriba.config"
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
when {
process {
"""
@@ -148,29 +496,33 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - arriba - log_final") },
- { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - arriba - log_out") },
- { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - arriba - log_progress") },
- { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - arriba - bam") },
- { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - arriba - bam_sorted") },
- { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - arriba - bam_transcript") },
- { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - arriba - bam_unsorted") },
- { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - arriba - bedgraph") },
- { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - arriba - fastq") },
- { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - arriba - junction") },
- { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - arriba - read_per_gene_tab") },
- { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - arriba - sam") },
- { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - arriba - spl_junc_tab") },
- { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - arriba - tab") },
- { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - arriba - wig") },
- { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - arriba - versions") }
+ { assert snapshot(process.out).match() }
)
}
}
- test("homo_sapiens - paired_end - starfusion") {
+ test("homo_sapiens - paired_end - starfusion - stub") {
+ options "-stub"
config "./nextflow.starfusion.config"
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
when {
process {
"""
@@ -196,29 +548,33 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_final") },
- { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_out") },
- { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_progress") },
- { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - starfusion - bam") },
- { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - starfusion - bam_sorted") },
- { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - starfusion - bam_transcript") },
- { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - starfusion - bam_unsorted") },
- { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - starfusion - bedgraph") },
- { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - starfusion - fastq") },
- { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - starfusion - junction") },
- { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - starfusion - read_per_gene_tab") },
- { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - starfusion - sam") },
- { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - starfusion - spl_junc_tab") },
- { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - starfusion - tab") },
- { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - starfusion - wig") },
- { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - starfusion - versions") }
+ { assert snapshot(process.out).match() }
)
}
}
- test("homo_sapiens - paired_end - multiple") {
+ test("homo_sapiens - paired_end - multiple - stub") {
+ options "-stub"
config "./nextflow.config"
+ setup {
+ run("STAR_GENOMEGENERATE") {
+ script "../../../star/genomegenerate/main.nf"
+ process {
+ """
+ input[0] = Channel.of([
+ [ id:'test_fasta' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+ ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
+ """
+ }
+ }
+ }
+
when {
process {
"""
@@ -246,22 +602,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - multiple - log_final") },
- { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - multiple - log_out") },
- { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - multiple - log_progress") },
- { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - multiple - bam") },
- { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - multiple - bam_sorted") },
- { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - multiple - bam_transcript") },
- { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - multiple - bam_unsorted") },
- { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - multiple - bedgraph") },
- { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - multiple - fastq") },
- { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - multiple - junction") },
- { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - multiple - read_per_gene_tab") },
- { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - multiple - sam") },
- { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - multiple - spl_junc_tab") },
- { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - multiple - tab") },
- { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - multiple - wig") },
- { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - multiple - versions") }
+ { assert snapshot(process.out).match() }
)
}
}
diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap
index 08edb914..c814eb56 100644
--- a/modules/nf-core/star/align/tests/main.nf.test.snap
+++ b/modules/nf-core/star/align/tests/main.nf.test.snap
@@ -1,382 +1,1170 @@
{
- "homo_sapiens - paired_end - multiple - bam_sorted": {
+ "homo_sapiens - single_end - stub": {
"content": [
- [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a"
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "10": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "11": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "12": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "13": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "14": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "15": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+ ],
+ "4": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ [
+ "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "5": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ [
+ "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "6": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "7": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "8": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ [
+ "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ]
+ ],
+ "9": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ [
+ "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "bam": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ [
+ "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "bam_sorted": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ [
+ "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "bam_transcript": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "bam_unsorted": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "bedgraph": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "fastq": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ [
+ "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ]
+ ],
+ "junction": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "log_final": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "log_out": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "log_progress": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "read_per_gene_tab": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "sam": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "spl_junc_tab": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "tab": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ [
+ "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+ ],
+ "wig": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
]
- ]
+ }
],
- "timestamp": "2023-12-04T18:01:19.968225733"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T15:16:04.712114"
},
- "homo_sapiens - paired_end - multiple - wig": {
+ "homo_sapiens - paired_end - arriba - stub": {
"content": [
- [
-
- ]
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
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+ [
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- [
-
- ]
- ],
- "timestamp": "2023-11-23T13:27:56.118974"
- },
- "homo_sapiens - paired_end - starfusion - read_per_gene_tab": {
- "content": [
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:27:56.264699"
- },
- "homo_sapiens - paired_end - multiple - log_progress": {
- "content": [
- "test.Log.progress.out"
- ],
- "timestamp": "2023-11-23T13:29:01.076947"
- },
- "homo_sapiens - paired_end - arriba - bam_unsorted": {
- "content": [
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:25:07.050409"
- },
- "homo_sapiens - paired_end - bam_sorted": {
- "content": [
+ ],
[
[
{
"id": "test",
"single_end": false
},
- "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f"
+ "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a"
]
- ]
- ],
- "timestamp": "2023-12-04T17:54:12.002180537"
- },
- "homo_sapiens - single_end - spl_junc_tab": {
- "content": [
+ ],
[
[
{
"id": "test",
- "single_end": true
+ "single_end": false
},
- "test.SJ.out.tab:md5,75a516ab950fb958f40b29996474949c"
+ "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a"
]
+ ],
+ [
+
+ ],
+ [
+ "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
]
],
- "timestamp": "2023-12-04T17:53:26.50932751"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T13:10:55.371956"
},
- "homo_sapiens - paired_end - starfusion - spl_junc_tab": {
+ "homo_sapiens - paired_end - arriba": {
"content": [
+ "test.Log.final.out",
+ "test.Log.out",
+ "test.Log.progress.out",
[
[
{
"id": "test",
"single_end": false
},
- "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a"
+ "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5"
]
- ]
- ],
- "timestamp": "2023-12-04T17:59:58.731699486"
- },
- "homo_sapiens - single_end - log_out": {
- "content": [
- "test.Log.out"
- ],
- "timestamp": "2023-11-23T13:22:55.126286"
- },
- "homo_sapiens - paired_end - log_final": {
- "content": [
- "test.Log.final.out"
- ],
- "timestamp": "2023-11-23T13:23:33.253884"
- },
- "homo_sapiens - single_end - log_final": {
- "content": [
- "test.Log.final.out"
- ],
- "timestamp": "2023-11-23T13:22:55.11799"
- },
- "homo_sapiens - paired_end - bam_transcript": {
- "content": [
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:23:33.287684"
- },
- "homo_sapiens - paired_end - starfusion - log_progress": {
- "content": [
- "test.Log.progress.out"
- ],
- "timestamp": "2023-11-23T13:27:55.971484"
- },
- "homo_sapiens - paired_end - multiple - bam_transcript": {
- "content": [
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:29:01.264176"
- },
- "homo_sapiens - paired_end - multiple - read_per_gene_tab": {
- "content": [
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:29:01.596406"
- },
- "homo_sapiens - single_end - read_per_gene_tab": {
- "content": [
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:22:55.205936"
- },
- "homo_sapiens - paired_end - junction": {
- "content": [
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:23:33.340653"
- },
- "homo_sapiens - paired_end - spl_junc_tab": {
- "content": [
+ ],
[
- [
- {
- "id": "test",
- "single_end": false
- },
- "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d"
- ]
- ]
- ],
- "timestamp": "2023-12-04T17:54:12.185730856"
- },
- "homo_sapiens - paired_end - starfusion - sam": {
- "content": [
+
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:27:56.300637"
- },
- "homo_sapiens - paired_end - arriba - bam": {
- "content": [
+ ],
+ [
+
+ ],
[
[
{
"id": "test",
"single_end": false
},
- "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5"
+ "test.SJ.out.tab:md5,5155c9fd1f787ad6d7d80987fb06219c"
]
- ]
- ],
- "timestamp": "2023-12-04T17:56:12.190560178"
- },
- "homo_sapiens - single_end - log_progress": {
- "content": [
+ ],
[
[
{
"id": "test",
- "single_end": true
+ "single_end": false
},
- "test.Log.progress.out:md5,b2bd061d6cbaaf3d6d3b1fed547f69b8"
+ "test.SJ.out.tab:md5,5155c9fd1f787ad6d7d80987fb06219c"
]
- ]
- ],
- "timestamp": "2023-12-04T17:53:26.450352138"
- },
- "homo_sapiens - paired_end - starfusion - wig": {
- "content": [
+ ],
[
- ]
- ],
- "timestamp": "2023-11-23T13:27:56.422018"
- },
- "homo_sapiens - paired_end - wig": {
- "content": [
+ ],
[
-
+ "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
]
],
- "timestamp": "2023-11-23T13:23:33.429457"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T13:05:10.7534"
},
- "homo_sapiens - paired_end - starfusion - log_out": {
+ "homo_sapiens - paired_end - starfusion - stub": {
"content": [
- "test.Log.out"
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "10": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "11": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "12": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "13": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "14": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "15": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+ ],
+ "4": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "5": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "6": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "7": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "8": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ]
+ ],
+ "9": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "bam": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "bam_sorted": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "bam_transcript": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "bam_unsorted": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "bedgraph": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "fastq": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+ "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+ ]
+ ]
+ ],
+ "junction": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "log_final": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "log_out": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "log_progress": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "read_per_gene_tab": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "sam": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "spl_junc_tab": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "tab": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f"
+ ],
+ "wig": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ }
],
- "timestamp": "2023-11-23T13:27:55.93945"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T15:16:40.64399"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test
index c17c8ba4..4d619c47 100644
--- a/modules/nf-core/star/genomegenerate/tests/main.nf.test
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test
@@ -28,15 +28,15 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") },
- { assert snapshot(process.out.versions).match("fasta_gtf_versions") }
+ { assert snapshot(
+ file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(),
+ process.out.versions)
+ .match() }
)
}
}
- test("fasta_gtf_stub") {
-
- options '-stub'
+ test("fasta") {
when {
process {
@@ -45,10 +45,7 @@ nextflow_process {
[ id:'test_fasta' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
])
- input[1] = Channel.of([
- [ id:'test_gtf' ],
- [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
- ])
+ input[1] = Channel.of([ [], [] ])
"""
}
}
@@ -56,13 +53,17 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") },
- { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") }
+ { assert snapshot(
+ file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(),
+ process.out.versions
+ ).match() }
)
}
}
- test("fasta") {
+ test("fasta_gtf_stub") {
+
+ options '-stub'
when {
process {
@@ -71,7 +72,10 @@ nextflow_process {
[ id:'test_fasta' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
])
- input[1] = Channel.of([ [], [] ])
+ input[1] = Channel.of([
+ [ id:'test_gtf' ],
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
+ ])
"""
}
}
@@ -79,11 +83,9 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") },
- { assert snapshot(process.out.versions).match("fasta_versions") }
+ { assert snapshot(process.out).match() }
)
}
-
}
test("fasta_stub") {
@@ -105,11 +107,8 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") },
- { assert snapshot(process.out.versions).match("fasta_stub_versions") }
+ { assert snapshot(process.out).match() }
)
}
-
}
-
}
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
index 5653d6e6..207f4b4f 100644
--- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
@@ -1,90 +1,148 @@
{
- "fasta_gtf_versions": {
+ "fasta_gtf": {
"content": [
+ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]",
[
"versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-02-01T15:54:31.798555"
+ "timestamp": "2024-07-22T14:55:35.478401"
},
- "fasta_stub_versions": {
+ "fasta_gtf_stub": {
"content": [
- [
- "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
- ]
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
- },
- "timestamp": "2024-02-01T15:55:07.521209"
- },
- "fasta_gtf_stub_index": {
- "content": [
- "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
- },
- "timestamp": "2024-02-01T15:54:46.478098"
- },
- "fasta_gtf_stub_versions": {
- "content": [
- [
- "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
- ]
+ {
+ "0": [
+ [
+ {
+ "id": "test_fasta"
+ },
+ [
+ "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+ ],
+ "index": [
+ [
+ {
+ "id": "test_fasta"
+ },
+ [
+ "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+ ]
+ }
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-02-01T15:54:46.491657"
+ "timestamp": "2024-07-22T14:55:57.247585"
},
- "fasta_index": {
+ "fasta_stub": {
"content": [
- "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]"
+ {
+ "0": [
+ [
+ {
+ "id": "test_fasta"
+ },
+ [
+ "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+ ],
+ "index": [
+ [
+ {
+ "id": "test_fasta"
+ },
+ [
+ "Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "SA:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+ ]
+ }
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-02-01T15:54:57.552329"
+ "timestamp": "2024-07-22T14:56:07.01742"
},
- "fasta_versions": {
+ "fasta": {
"content": [
+ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]",
[
"versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
]
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
- },
- "timestamp": "2024-02-01T15:54:57.560541"
- },
- "fasta_gtf_index": {
- "content": [
- "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
- },
- "timestamp": "2024-02-01T15:54:31.786814"
- },
- "fasta_stub_index": {
- "content": [
- "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]"
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.04.3"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-02-01T15:55:07.517472"
+ "timestamp": "2024-07-22T14:55:45.48784"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test
index 00efe8f1..2204e849 100644
--- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test
+++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_process {
name "Test Process STRINGTIE_STRINGTIE"
script "../main.nf"
process "STRINGTIE_STRINGTIE"
+ config "./nextflow.config"
tag "modules"
tag "modules_nfcore"
tag "stringtie"
@@ -10,8 +11,6 @@ nextflow_process {
test("sarscov2 [bam] - forward strandedness") {
- config "./nextflow.config"
-
when {
process {
"""
@@ -27,17 +26,17 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(process.out.transcript_gtf).match("fs_transcript_gtf") },
- { assert snapshot(process.out.abundance).match("fs_abundance") },
- { assert snapshot(process.out.versions).match("fs_versions") }
+ { assert snapshot(
+ process.out.abundance,
+ process.out.transcript_gtf,
+ process.out.versions
+ ).match() }
)
}
}
test("sarscov2 [bam] - forward strandedness + reference annotation") {
- config "./nextflow.config"
-
when {
process {
"""
@@ -53,18 +52,18 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(process.out.transcript_gtf).match("fs_gtf_transcript_gtf") },
- { assert snapshot(process.out.abundance).match("fs_gtf_abundance") },
- { assert snapshot(process.out.ballgown).match("fs_gtf_ballgown") },
- { assert snapshot(process.out.versions).match("fs_gtf_versions") }
+ { assert snapshot(
+ process.out.abundance,
+ process.out.ballgown,
+ process.out.transcript_gtf,
+ process.out.versions
+ ).match() }
)
}
}
test("sarscov2 [bam] - reverse strandedness") {
- config "./nextflow.config"
-
when {
process {
"""
@@ -80,16 +79,117 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(process.out.transcript_gtf).match("rs_transcript_gtf") },
- { assert snapshot(process.out.abundance).match("rs_abundance") },
- { assert snapshot(process.out.versions).match("rs_versions") }
+ { assert snapshot(
+ process.out.abundance,
+ process.out.transcript_gtf,
+ process.out.versions
+ ).match() }
)
}
}
test("sarscov2 [bam] - reverse strandedness + reference annotation") {
- config "./nextflow.config"
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', strandedness:'reverse' ], // meta map
+ [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+ ]
+ input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.abundance,
+ process.out.ballgown,
+ process.out.transcript_gtf,
+ process.out.versions
+ ).match() }
+ )
+ }
+ }
+
+ test("sarscov2 [bam] - forward strandedness - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', strandedness:'forward' ], // meta map
+ [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+ ]
+ input[1] = []
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("sarscov2 [bam] - forward strandedness + reference annotation - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', strandedness:'forward' ], // meta map
+ [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+ ]
+ input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("sarscov2 [bam] - reverse strandedness - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', strandedness:'reverse' ], // meta map
+ [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+ ]
+ input[1] = []
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("sarscov2 [bam] - reverse strandedness + reference annotation - stub") {
+
+ options "-stub"
when {
process {
@@ -106,10 +206,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
- { assert snapshot(process.out.transcript_gtf).match("rs_gtf_transcript_gtf") },
- { assert snapshot(process.out.abundance).match("rs_gtf_abundance") },
- { assert snapshot(process.out.ballgown).match("rs_gtf_ballgown") },
- { assert snapshot(process.out.versions).match("rs_gtf_versions") }
+ { assert snapshot(process.out).match() }
)
}
}
diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
index bf751636..124dd4cb 100644
--- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
+++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
{
- "fs_abundance": {
+ "sarscov2 [bam] - forward strandedness + reference annotation": {
"content": [
[
[
@@ -7,49 +7,44 @@
"id": "test",
"strandedness": "forward"
},
- "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3"
+ "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e"
]
- ]
- ],
- "timestamp": "2023-11-23T13:55:41.032044613"
- },
- "fs_transcript_gtf": {
- "content": [
+ ],
[
[
{
"id": "test",
"strandedness": "forward"
},
- "test.transcripts.gtf:md5,569137af5be452413086b50653a97203"
+ [
+ "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540",
+ "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471",
+ "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4",
+ "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f",
+ "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818"
+ ]
]
- ]
- ],
- "timestamp": "2023-11-23T13:55:41.017978904"
- },
- "rs_abundance": {
- "content": [
+ ],
[
[
{
"id": "test",
- "strandedness": "reverse"
+ "strandedness": "forward"
},
- "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3"
+ "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04"
]
- ]
- ],
- "timestamp": "2023-11-23T13:56:13.601112933"
- },
- "fs_gtf_versions": {
- "content": [
+ ],
[
"versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
]
],
- "timestamp": "2023-11-23T13:56:00.523797974"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T12:33:44.299962"
},
- "fs_gtf_transcript_gtf": {
+ "sarscov2 [bam] - forward strandedness": {
"content": [
[
[
@@ -57,50 +52,395 @@
"id": "test",
"strandedness": "forward"
},
- "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04"
+ "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3"
+ ]
+ ],
+ [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.transcripts.gtf:md5,569137af5be452413086b50653a97203"
]
+ ],
+ [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
]
],
- "timestamp": "2023-11-23T13:56:00.475164879"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T12:33:35.177738"
},
- "rs_versions": {
+ "sarscov2 [bam] - forward strandedness - stub": {
"content": [
- [
- "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
- ]
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "4": [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+ ],
+ "abundance": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "ballgown": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "coverage_gtf": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "transcript_gtf": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+ ]
+ }
],
- "timestamp": "2023-11-23T13:56:13.623892691"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T12:36:32.885078"
},
- "rs_gtf_transcript_gtf": {
+ "sarscov2 [bam] - forward strandedness + reference annotation - stub": {
"content": [
- [
- [
- {
- "id": "test",
- "strandedness": "reverse"
- },
- "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa"
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "4": [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+ ],
+ "abundance": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "ballgown": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "coverage_gtf": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "transcript_gtf": [
+ [
+ {
+ "id": "test",
+ "strandedness": "forward"
+ },
+ "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
]
- ]
+ }
],
- "timestamp": "2023-11-23T13:56:22.693599559"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T12:36:43.325777"
},
- "fs_gtf_abundance": {
+ "sarscov2 [bam] - reverse strandedness + reference annotation - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "4": [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+ ],
+ "abundance": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "ballgown": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "coverage_gtf": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "transcript_gtf": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T12:37:06.085936"
+ },
+ "sarscov2 [bam] - reverse strandedness - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "4": [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+ ],
+ "abundance": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "ballgown": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "coverage_gtf": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "transcript_gtf": [
+ [
+ {
+ "id": "test",
+ "strandedness": "reverse"
+ },
+ "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T12:36:53.837578"
+ },
+ "sarscov2 [bam] - reverse strandedness + reference annotation": {
"content": [
[
[
{
"id": "test",
- "strandedness": "forward"
+ "strandedness": "reverse"
},
- "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e"
+ "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce"
]
- ]
- ],
- "timestamp": "2023-11-23T13:56:00.482135418"
- },
- "rs_gtf_ballgown": {
- "content": [
+ ],
[
[
{
@@ -115,72 +455,54 @@
"t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818"
]
]
- ]
- ],
- "timestamp": "2023-11-23T13:56:22.715698347"
- },
- "rs_transcript_gtf": {
- "content": [
+ ],
[
[
{
"id": "test",
"strandedness": "reverse"
},
- "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f"
+ "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa"
]
- ]
- ],
- "timestamp": "2023-11-23T13:56:13.590054035"
- },
- "rs_gtf_versions": {
- "content": [
+ ],
[
"versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
]
],
- "timestamp": "2023-11-23T13:56:22.725513476"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T12:34:03.114695"
},
- "fs_gtf_ballgown": {
+ "sarscov2 [bam] - reverse strandedness": {
"content": [
[
[
{
"id": "test",
- "strandedness": "forward"
+ "strandedness": "reverse"
},
- [
- "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540",
- "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471",
- "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4",
- "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f",
- "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818"
- ]
+ "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3"
]
- ]
- ],
- "timestamp": "2023-11-23T13:56:00.494299817"
- },
- "fs_versions": {
- "content": [
- [
- "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
- ]
- ],
- "timestamp": "2023-11-23T13:55:41.049417582"
- },
- "rs_gtf_abundance": {
- "content": [
+ ],
[
[
{
"id": "test",
"strandedness": "reverse"
},
- "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce"
+ "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f"
]
+ ],
+ [
+ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38"
]
],
- "timestamp": "2023-11-23T13:56:22.701059059"
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-22T12:33:52.874479"
}
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml
index c4235872..b9644de9 100644
--- a/modules/nf-core/tabix/bgziptabix/environment.yml
+++ b/modules/nf-core/tabix/bgziptabix/environment.yml
@@ -5,4 +5,4 @@ channels:
- defaults
dependencies:
- bioconda::tabix=1.11
- - bioconda::htslib=1.19.1
+ - bioconda::htslib=1.20
diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
index bcdcf2a6..05041f49 100644
--- a/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -4,8 +4,8 @@ process TABIX_BGZIPTABIX {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' :
- 'biocontainers/htslib:1.19.1--h81da01d_1' }"
+ 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' :
+ 'biocontainers/htslib:1.20--h5efdd21_2' }"
input:
tuple val(meta), path(input)
@@ -24,7 +24,7 @@ process TABIX_BGZIPTABIX {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz
- tabix $args2 ${prefix}.${input.getExtension()}.gz
+ tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
index 87ea2c84..1a84d74f 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
"""
input[0] = [
[ id:'tbi_test' ],
- [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
]
"""
}
@@ -43,7 +43,7 @@ nextflow_process {
"""
input[0] = [
[ id:'csi_test' ],
- [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
]
"""
}
@@ -72,7 +72,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
- [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
]
"""
}
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
index fcecb2e4..c166ea72 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
@@ -8,14 +8,14 @@
"id": "tbi_test"
},
"tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
- "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4"
+ "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c"
]
],
"1": [
],
"2": [
- "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+ "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
],
"gz_csi": [
@@ -26,15 +26,19 @@
"id": "tbi_test"
},
"tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
- "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4"
+ "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c"
]
],
"versions": [
- "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+ "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
]
}
],
- "timestamp": "2024-02-19T14:50:51.513838"
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-19T11:29:16.053817543"
},
"sarscov2_bed_csi": {
"content": [
@@ -48,11 +52,11 @@
"id": "csi_test"
},
"csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
- "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43"
+ "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5"
]
],
"2": [
- "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+ "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
],
"gz_csi": [
[
@@ -60,35 +64,51 @@
"id": "csi_test"
},
"csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
- "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43"
+ "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5"
]
],
"gz_tbi": [
],
"versions": [
- "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+ "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
]
}
],
- "timestamp": "2024-02-19T14:51:00.513777"
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-19T11:29:27.667745444"
},
"csi_test": {
"content": [
"csi_test.bed.gz"
],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
"timestamp": "2024-02-19T14:51:00.548801"
},
"csi_stub": {
"content": [
"test.bed.gz"
],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
"timestamp": "2024-02-19T14:51:09.218454"
},
"tbi_test": {
"content": [
"tbi_test.bed.gz"
],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
"timestamp": "2024-02-19T14:50:51.579654"
},
"sarscov2_bed_csi_stub": {
@@ -113,7 +133,7 @@
]
],
"2": [
- "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+ "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
],
"gz_csi": [
[
@@ -134,10 +154,14 @@
]
],
"versions": [
- "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
+ "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
]
}
],
- "timestamp": "2024-02-19T14:51:09.164254"
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-19T11:29:45.105209991"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml
index 76b45e16..4d1f9dd4 100644
--- a/modules/nf-core/tabix/tabix/environment.yml
+++ b/modules/nf-core/tabix/tabix/environment.yml
@@ -1,8 +1,10 @@
name: tabix_tabix
+
channels:
- conda-forge
- bioconda
- defaults
+
dependencies:
+ - bioconda::htslib=1.20
- bioconda::tabix=1.11
- - bioconda::htslib=1.19.1
diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 1737141d..13acd670 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -4,8 +4,8 @@ process TABIX_TABIX {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' :
- 'biocontainers/htslib:1.19.1--h81da01d_1' }"
+ 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' :
+ 'biocontainers/htslib:1.20--h5efdd21_2' }"
input:
tuple val(meta), path(tab)
@@ -21,7 +21,10 @@ process TABIX_TABIX {
script:
def args = task.ext.args ?: ''
"""
- tabix $args $tab
+ tabix \\
+ --threads $task.cpus \\
+ $args \\
+ $tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -33,8 +36,8 @@ process TABIX_TABIX {
"""
touch ${tab}.tbi
touch ${tab}.csi
- cat <<-END_VERSIONS > versions.yml
+ cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 3a150c70..102b0d7b 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
"""
input[0] = [
[ id:'tbi_bed' ],
- [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ]
]
"""
}
@@ -25,11 +25,10 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out).match() },
{ assert snapshot(
- file(process.out.tbi[0][1]).name
- ).match("tbi_bed")
- }
+ process.out,
+ file(process.out.tbi[0][1]).name
+ ).match() }
)
}
}
@@ -41,7 +40,7 @@ nextflow_process {
"""
input[0] = [
[ id:'tbi_gff' ],
- [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ]
]
"""
}
@@ -50,11 +49,9 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out).match() },
{ assert snapshot(
- file(process.out.tbi[0][1]).name
- ).match("tbi_gff")
- }
+ process.out,
+ file(process.out.tbi[0][1]).name).match() }
)
}
@@ -67,7 +64,7 @@ nextflow_process {
"""
input[0] = [
[ id:'tbi_vcf' ],
- [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
]
"""
}
@@ -76,11 +73,10 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out).match() },
{ assert snapshot(
- file(process.out.tbi[0][1]).name
- ).match("tbi_vcf")
- }
+ process.out,
+ file(process.out.tbi[0][1]).name
+ ).match() }
)
}
@@ -93,7 +89,7 @@ nextflow_process {
"""
input[0] = [
[ id:'vcf_csi' ],
- [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
]
"""
}
@@ -102,11 +98,10 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out).match() },
{ assert snapshot(
- file(process.out.csi[0][1]).name
- ).match("vcf_csi")
- }
+ process.out,
+ file(process.out.csi[0][1]).name
+ ).match() }
)
}
@@ -120,7 +115,7 @@ nextflow_process {
"""
input[0] = [
[ id:'vcf_csi_stub' ],
- [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
]
"""
}
@@ -129,11 +124,10 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out).match() },
{ assert snapshot(
- file(process.out.csi[0][1]).name
- ).match("vcf_csi_stub")
- }
+ process.out,
+ file(process.out.csi[0][1]).name
+ ).match() }
)
}
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
index 034e38b6..c2b9ed0b 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -1,16 +1,4 @@
{
- "vcf_csi_stub": {
- "content": [
- "test.vcf.gz.csi"
- ],
- "timestamp": "2024-03-04T14:51:59.788002"
- },
- "tbi_gff": {
- "content": [
- "genome.gff3.gz.tbi"
- ],
- "timestamp": "2024-02-19T14:53:37.420216"
- },
"sarscov2_gff_tbi": {
"content": [
{
@@ -19,14 +7,14 @@
{
"id": "tbi_gff"
},
- "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178"
+ "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
]
],
"1": [
],
"2": [
- "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
],
"csi": [
@@ -36,15 +24,20 @@
{
"id": "tbi_gff"
},
- "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178"
+ "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
]
],
"versions": [
- "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
]
- }
+ },
+ "genome.gff3.gz.tbi"
],
- "timestamp": "2024-02-19T14:53:37.388157"
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-19T12:06:25.653807564"
},
"sarscov2_bedgz_tbi": {
"content": [
@@ -54,14 +47,14 @@
{
"id": "tbi_bed"
},
- "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8"
+ "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
]
],
"1": [
],
"2": [
- "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
],
"csi": [
@@ -71,27 +64,20 @@
{
"id": "tbi_bed"
},
- "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8"
+ "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
]
],
"versions": [
- "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
]
- }
- ],
- "timestamp": "2024-02-19T14:53:28.879408"
- },
- "tbi_vcf": {
- "content": [
- "test.vcf.gz.tbi"
- ],
- "timestamp": "2024-02-19T14:53:46.402522"
- },
- "vcf_csi": {
- "content": [
- "test.vcf.gz.csi"
+ },
+ "test.bed.gz.tbi"
],
- "timestamp": "2024-02-19T14:53:54.921189"
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-19T12:06:09.754082161"
},
"sarscov2_vcf_tbi": {
"content": [
@@ -101,14 +87,14 @@
{
"id": "tbi_vcf"
},
- "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf"
+ "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
]
],
"1": [
],
"2": [
- "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
],
"csi": [
@@ -118,15 +104,20 @@
{
"id": "tbi_vcf"
},
- "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf"
+ "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
]
],
"versions": [
- "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
]
- }
+ },
+ "test.vcf.gz.tbi"
],
- "timestamp": "2024-02-19T14:53:46.370358"
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-19T12:06:40.042648294"
},
"sarscov2_vcf_csi_stub": {
"content": [
@@ -148,7 +139,7 @@
]
],
"2": [
- "versions.yml:md5,3d45df6d80883bad358631069a2940fd"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
],
"csi": [
[
@@ -167,11 +158,16 @@
]
],
"versions": [
- "versions.yml:md5,3d45df6d80883bad358631069a2940fd"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
]
- }
+ },
+ "test.vcf.gz.csi"
],
- "timestamp": "2024-03-04T14:51:59.766184"
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-19T12:07:08.700367261"
},
"sarscov2_vcf_csi": {
"content": [
@@ -184,34 +180,33 @@
{
"id": "vcf_csi"
},
- "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03"
+ "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b"
]
],
"2": [
- "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
],
"csi": [
[
{
"id": "vcf_csi"
},
- "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03"
+ "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b"
]
],
"tbi": [
],
"versions": [
- "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3"
+ "versions.yml:md5,07064637fb8a217174052be8e40234e2"
]
- }
- ],
- "timestamp": "2024-02-19T14:53:54.886876"
- },
- "tbi_bed": {
- "content": [
- "test.bed.gz.tbi"
+ },
+ "test.vcf.gz.csi"
],
- "timestamp": "2024-02-19T14:53:28.947628"
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-07-19T12:06:55.362067748"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
index 0c9cbb10..4f498244 100644
--- a/modules/nf-core/untar/environment.yml
+++ b/modules/nf-core/untar/environment.yml
@@ -1,11 +1,9 @@
name: untar
-
channels:
- conda-forge
- bioconda
- defaults
-
dependencies:
- conda-forge::grep=3.11
- - conda-forge::sed=4.7
+ - conda-forge::sed=4.8
- conda-forge::tar=1.34
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index 8a75bb95..9bd8f554 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -4,8 +4,8 @@ process UNTAR {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'nf-core/ubuntu:20.04' }"
+ 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
+ 'nf-core/ubuntu:22.04' }"
input:
tuple val(meta), path(archive)
@@ -52,8 +52,29 @@ process UNTAR {
stub:
prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
"""
- mkdir $prefix
- touch ${prefix}/file.txt
+ mkdir ${prefix}
+ ## Dry-run untaring the archive to get the files and place all in prefix
+ if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+ for i in `tar -tf ${archive}`;
+ do
+ if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]];
+ then
+ touch \${i}
+ else
+ mkdir -p \${i}
+ fi
+ done
+ else
+ for i in `tar -tf ${archive}`;
+ do
+ if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]];
+ then
+ touch ${prefix}/\${i}
+ else
+ mkdir -p ${prefix}/\${i}
+ fi
+ done
+ fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index 2a7c97bf..c957517a 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -6,6 +6,7 @@ nextflow_process {
tag "modules"
tag "modules_nfcore"
tag "untar"
+
test("test_untar") {
when {
@@ -19,10 +20,9 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out.untar).match("test_untar") },
+ { assert snapshot(process.out).match() },
)
}
-
}
test("test_untar_onlyfiles") {
@@ -38,10 +38,48 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
- { assert snapshot(process.out.untar).match("test_untar_onlyfiles") },
+ { assert snapshot(process.out).match() },
)
}
+ }
+
+ test("test_untar - stub") {
+
+ options "-stub"
+ when {
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() },
+ )
+ }
}
+ test("test_untar_onlyfiles - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+
+ then {
+ assertAll (
+ { assert process.success },
+ { assert snapshot(process.out).match() },
+ )
+ }
+ }
}
diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
index 64550292..ceb91b79 100644
--- a/modules/nf-core/untar/tests/main.nf.test.snap
+++ b/modules/nf-core/untar/tests/main.nf.test.snap
@@ -1,42 +1,158 @@
{
"test_untar_onlyfiles": {
"content": [
- [
- [
+ {
+ "0": [
[
-
- ],
+ [
+
+ ],
+ [
+ "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+ ],
+ "untar": [
+ [
+ [
+
+ ],
+ [
+ "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-10T12:04:28.231047"
+ },
+ "test_untar_onlyfiles - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ [
+
+ ],
+ [
+ "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+ ],
+ "untar": [
[
- "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+ [
+
+ ],
+ [
+ "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
]
+ ],
+ "versions": [
+ "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
]
- ]
+ }
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-02-28T11:49:41.320643"
+ "timestamp": "2024-07-10T12:04:45.773103"
+ },
+ "test_untar - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ [
+
+ ],
+ [
+ "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+ ],
+ "untar": [
+ [
+ [
+
+ ],
+ [
+ "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+ "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.3"
+ },
+ "timestamp": "2024-07-10T12:04:36.777441"
},
"test_untar": {
"content": [
- [
- [
+ {
+ "0": [
[
-
- ],
+ [
+
+ ],
+ [
+ "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
+ "opts.k2d:md5,a033d00cf6759407010b21700938f543",
+ "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+ ],
+ "untar": [
[
- "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
- "opts.k2d:md5,a033d00cf6759407010b21700938f543",
- "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+ [
+
+ ],
+ [
+ "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
+ "opts.k2d:md5,a033d00cf6759407010b21700938f543",
+ "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+ ]
]
+ ],
+ "versions": [
+ "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
]
- ]
+ }
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nextflow": "24.04.3"
},
- "timestamp": "2024-02-28T11:49:33.795172"
+ "timestamp": "2024-07-10T12:04:19.377674"
}
}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 5c334c80..e1bedd5f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,15 +14,20 @@ params {
// References
genome = 'GRCh38'
+ gencode_annotation_version = 37
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
save_reference = true
fasta = null
fai = null
+ gtf = null
star_index = null
transcript_fasta = null
salmon_index = null
sequence_dict = null
+ skip_download_vep = true
+ skip_download_gnomad = true
+ vep_refs_download = null
// Main options
platform = 'illumina'
@@ -54,6 +59,8 @@ params {
// Variant annotation
vep_cache_version = 110
+ vep_cache = null
+ vep_plugin_files = null
// MultiQC options
multiqc_config = null
@@ -277,7 +284,7 @@ manifest {
description = """Pipeline to analyse RNAseq from raredisease patients"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '2.1.0'
+ version = '2.2.0'
doi = '10.5281/zenodo.10828946'
}
@@ -288,6 +295,7 @@ includeConfig 'conf/modules/analyse_transcripts.config'
includeConfig 'conf/modules/annotate_snv.config'
includeConfig 'conf/modules/bam_qc.config'
includeConfig 'conf/modules/call_variants.config'
+includeConfig 'conf/modules/download_references.config'
includeConfig 'conf/modules/igv_tracks.config'
includeConfig 'conf/modules/general_tomte.config'
includeConfig 'conf/modules/prepare_references.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index bd08defe..aa6f52f6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -27,7 +27,8 @@
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
- "fa_icon": "fas fa-folder-open"
+ "fa_icon": "fas fa-folder-open",
+ "default": "results"
},
"email": {
"type": "string",
@@ -44,7 +45,8 @@
"save_mapped_as_cram": {
"type": "boolean",
"description": "Do you want to save bam as cram",
- "fa_icon": "far fa-file-archive"
+ "fa_icon": "far fa-file-archive",
+ "default": true
}
}
},
@@ -56,10 +58,11 @@
"properties": {
"genome": {
"type": "string",
- "description": "Name of iGenomes reference, etiher hg19/GRCh37 or hg38/GRCh38, it is case sensitive.",
+ "description": "Name of genome reference, etiher hg19/GRCh37 or hg38/GRCh38, it is case sensitive.",
"fa_icon": "fas fa-book",
"enum": ["hg19", "GRCh37", "hg38", "GRCh38"],
- "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
+ "help_text": "If using a reference genome configured in the pipeline using iGenomes, use `--igenomes_base` to provide a path, or you want to automatically download all required files, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.",
+ "default": "GRCh38"
},
"fasta": {
"type": "string",
@@ -68,7 +71,7 @@
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
- "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a STAR index available this will be generated for you automatically. Combine with `--save_reference` to save STAR index for future runs.",
+ "help_text": "If none provided, will be downloaded from gencode according to `--genome` and `--gencode_annotation_version`.",
"fa_icon": "far fa-file-code"
},
"fai": {
@@ -87,7 +90,14 @@
"pattern": "^\\S+\\.gtf(\\.gz)?$",
"description": "Path to GTF annotation file.",
"fa_icon": "fas fa-code-branch",
- "help_text": "This parameter is *mandatory* if `--genome` is not specified."
+ "help_text": "If none provided, will be downloaded from gencode according to `--genome` and `--gencode_annotation_version`."
+ },
+ "gencode_annotation_version": {
+ "type": "integer",
+ "default": 37,
+ "description": "Name of Genomes gencode reference version to download if fasta or gtf is not provided.",
+ "fa_icon": "fas fa-book",
+ "help_text": "If fasta or gtf is not provided the gencode version specified will be downloaded. Combine with `--save_reference` to save gtf and/or fasta for future runs."
},
"igenomes_ignore": {
"type": "boolean",
@@ -107,7 +117,8 @@
"type": "boolean",
"description": "If generated by the pipeline save the required indices/references in the results directory.",
"help_text": "The saved references can be used for future pipeline runs, reducing processing times.",
- "fa_icon": "fas fa-save"
+ "fa_icon": "fas fa-save",
+ "default": true
},
"sequence_dict": {
"type": "string",
@@ -163,9 +174,26 @@
"pattern": "^\\S+\\.csv$",
"mimetype": "text/csv",
"schema": "assets/vep_plugin_files_schema.json"
+ },
+ "skip_download_vep": {
+ "type": "boolean",
+ "default": true,
+ "fa_icon": "fas fa-toggle-on",
+ "description": "Skip vep cache download."
+ },
+ "skip_download_gnomad": {
+ "type": "boolean",
+ "default": true,
+ "description": "Skip gnomad reference download for vep.",
+ "fa_icon": "fas fa-toggle-on"
+ },
+ "vep_refs_download": {
+ "type": "string",
+ "description": "Path to comma separated csv with paths to vep references to download, see example in test_data/vep_to_download.csv",
+ "fa_icon": "fas fa-file-csv",
+ "format": "file-path"
}
- },
- "required": ["fasta", "gtf"]
+ }
},
"trimming_options": {
"title": "Trimming options",
diff --git a/subworkflows/local/allele_specific_calling.nf b/subworkflows/local/allele_specific_calling.nf
index 296da783..b4a6aade 100644
--- a/subworkflows/local/allele_specific_calling.nf
+++ b/subworkflows/local/allele_specific_calling.nf
@@ -50,8 +50,7 @@ workflow ALLELE_SPECIFIC_CALLING {
)
BOOTSTRAPANN(
- ch_ind_vcf_tbi,
- GATK4_ASEREADCOUNTER.out.csv
+ ch_ind_vcf_tbi.join(GATK4_ASEREADCOUNTER.out.csv),
)
TABIX_BGZIPTABIX(BOOTSTRAPANN.out.vcf)
diff --git a/subworkflows/local/download_references.nf b/subworkflows/local/download_references.nf
new file mode 100644
index 00000000..29728066
--- /dev/null
+++ b/subworkflows/local/download_references.nf
@@ -0,0 +1,50 @@
+//
+// Download reference files
+//
+
+include { GENCODE_DOWNLOAD as FASTA_DOWNLOAD } from '../../modules/local/gencode_download'
+include { GENCODE_DOWNLOAD as GTF_DOWNLOAD } from '../../modules/local/gencode_download'
+include { WGET_DOWNLOAD as WGET_DOWNLOAD } from '../../modules/local/wget_download'
+include { VEP_GNOMAD_DOWNLOAD } from '../../modules/local/vep_gnomad_download'
+include { BUILD_VEP_CACHE } from '../../modules/local/build_vep_cache'
+
+workflow DOWNLOAD_REFERENCES {
+ take:
+ ch_genome // channel: [mandatory] val(genome)
+ ch_gencode_annotation_version // channel: [mandatory] val(gencode_annotation_version)
+ ch_vep_refs_download_unprocessed // channel: [optional] val(path_to_csv)
+ ch_vep_cache_version // channel: [optional] val(vep_cache_version)
+
+ main:
+ ch_versions = Channel.empty()
+
+ // Download fasta if not provided
+ FASTA_DOWNLOAD(ch_genome, ch_gencode_annotation_version, "fasta")
+
+ // Download gtf if not provided
+ GTF_DOWNLOAD(ch_genome, ch_gencode_annotation_version, "gtf")
+
+ // Read and store paths in vep_refs_download_unprocessed
+ ch_vep_refs_download_unprocessed.splitCsv(header: true)
+ .map { row -> return tuple(row.name, row.path_for_wget) }
+ .set { ch_vep_refs_download }
+
+ // Download files
+ WGET_DOWNLOAD(ch_vep_refs_download.filter{ it != null })
+ VEP_GNOMAD_DOWNLOAD(ch_genome, ch_vep_cache_version)
+
+ BUILD_VEP_CACHE(WGET_DOWNLOAD.out.downloaded_file.collect(), VEP_GNOMAD_DOWNLOAD.out.gnomad_vcf_tbi.flatten().collect())
+
+ ch_versions = ch_versions.mix(FASTA_DOWNLOAD.out.versions)
+ ch_versions = ch_versions.mix(GTF_DOWNLOAD.out.versions)
+ ch_versions = ch_versions.mix(WGET_DOWNLOAD.out.versions)
+ ch_versions = ch_versions.mix(VEP_GNOMAD_DOWNLOAD.out.versions)
+
+
+ emit:
+ fasta = FASTA_DOWNLOAD.out.fasta // channel: [ path(fasta) ]
+ gtf = GTF_DOWNLOAD.out.gtf // channel: [ path(gtf) ]
+ vep_cache = BUILD_VEP_CACHE.out.vep_cache // channel: [ path(vep_cache) ]
+ vep_plugin = BUILD_VEP_CACHE.out.vep_plugin_file // channel: [ path(vep_plugin) ]
+ versions = ch_versions // channel: [ path(versions.yml) ]
+}
diff --git a/test_data/vep_to_download.csv b/test_data/vep_to_download.csv
new file mode 100644
index 00000000..1819a0d8
--- /dev/null
+++ b/test_data/vep_to_download.csv
@@ -0,0 +1,4 @@
+name,path_for_wget
+clinvar_20240806.vcf.gz,ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/clinvar.vcf.gz
+clinvar_20240806.vcf.gz.tbi,ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/clinvar.vcf.gz.tbi
+homo_sapiens_merged,https://ftp.ensembl.org/pub/release-110/variation/indexed_vep_cache/homo_sapiens_merged_vep_110_GRCh38.tar.gz
diff --git a/workflows/tomte.nf b/workflows/tomte.nf
index 9d00ea20..d16a1bef 100644
--- a/workflows/tomte.nf
+++ b/workflows/tomte.nf
@@ -13,6 +13,7 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi
//
// SUBWORKFLOW: local
//
+include { DOWNLOAD_REFERENCES } from '../subworkflows/local/download_references'
include { PREPARE_REFERENCES } from '../subworkflows/local/prepare_references'
include { ALIGNMENT } from '../subworkflows/local/alignment'
include { BAM_QC } from '../subworkflows/local/bam_qc'
@@ -53,12 +54,30 @@ workflow TOMTE {
// Mandatory
ch_samples = ch_samplesheet.map { meta, fastqs -> meta }
ch_case_info = ch_samples.toList().map { create_case_channel(it) }
- ch_fasta = Channel.fromPath(params.fasta).map {it -> [[id:it[0].simpleName], it]}.collect()
- ch_gtf = Channel.fromPath(params.gtf).map {it -> [[id:it[0].simpleName], it]}.collect()
ch_platform = Channel.from(params.platform).collect()
ch_foundin_header = Channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect()
// Optional
+ ch_vep_refs_download_unprocessed = params.vep_refs_download ? Channel.fromPath(params.vep_refs_download)
+ : Channel.empty()
+
+ DOWNLOAD_REFERENCES(
+ params.genome,
+ params.gencode_annotation_version,
+ ch_vep_refs_download_unprocessed,
+ params.vep_cache_version
+ ).set { downloads }
+ ch_versions = ch_versions.mix(DOWNLOAD_REFERENCES.out.versions)
+
+ // Optional
+ ch_fasta = params.fasta ? Channel.fromPath(params.fasta).map {it -> [[id:it[0].simpleName], it]}.collect()
+ : downloads.fasta.map {it -> [[id:it[0].simpleName], it]}.collect()
+ ch_gtf = params.gtf ? Channel.fromPath(params.gtf).map {it -> [[id:it[0].simpleName], it]}.collect()
+ : downloads.gtf.map {it -> [[id:it[0].simpleName], it]}.collect()
+ ch_vep_cache_unprocessed = params.vep_cache ? Channel.fromPath(params.vep_cache)
+ : Channel.empty().mix(downloads.vep_cache)
+ ch_vep_extra_files_unsplit = params.vep_plugin_files ? Channel.fromPath(params.vep_plugin_files)
+ : Channel.empty().mix(downloads.vep_plugin)
ch_fai = params.fai ? Channel.fromPath(params.fai).map {it -> [[id:it[0].simpleName], it]}.collect()
: Channel.empty()
ch_gene_panel_clinical_filter = params.gene_panel_clinical_filter ? Channel.fromPath(params.gene_panel_clinical_filter).collect()
@@ -79,24 +98,25 @@ workflow TOMTE {
: Channel.empty()
ch_subsample_bed = params.subsample_bed ? Channel.fromPath(params.subsample_bed).collect()
: Channel.empty()
- ch_vep_cache_unprocessed = params.vep_cache ? Channel.fromPath(params.vep_cache)
- : Channel.empty()
- ch_vep_extra_files_unsplit = params.vep_plugin_files ? Channel.fromPath(params.vep_plugin_files).collect()
- : Channel.value([])
-
// Read and store paths in the vep_plugin_files file
- ch_vep_extra_files_unsplit.splitCsv ( header:true )
- .map { row ->
- f = file(row.vep_files[0])
- if(f.isFile() || f.isDirectory()){
- return [f]
+ ch_vep_extra_files_unsplit.splitCsv(header: true)
+ .flatMap { row ->
+ row.vep_files.split(',').collect { file(it.trim()) }
+ }
+ .map { path ->
+ if (params.skip_download_vep) {
+ if(path.isFile() || path.isDirectory()) {
+ return path
} else {
- error("\nVep database file ${f} does not exist.")
+ error("\nVep database file ${path} does not exist.")
}
+ } else {
+ return path
}
- .collect()
- .set {ch_vep_extra_files}
+ }
+ .collect()
+ .set { ch_vep_extra_files }
PREPARE_REFERENCES(
ch_fasta,
@@ -108,6 +128,7 @@ workflow TOMTE {
ch_salmon_index,
ch_sequence_dict
).set { ch_references }
+ ch_versions = ch_versions.mix(PREPARE_REFERENCES.out.versions.first())
FASTQC (
ch_samplesheet
@@ -234,7 +255,9 @@ workflow TOMTE {
ch_multiqc_files.collect(),
ch_multiqc_config.toList(),
ch_multiqc_custom_config.toList(),
- ch_multiqc_logo.toList()
+ ch_multiqc_logo.toList(),
+ [],
+ []
)
emit: