-
Notifications
You must be signed in to change notification settings - Fork 714
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'nf-core:master' into shigapass
- Loading branch information
Showing
12 changed files
with
395 additions
and
588 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,174 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process PARABRICKS_FQ2BAM" | ||
| script "../main.nf" | ||
| process "PARABRICKS_FQ2BAM" | ||
| config "./nextflow.config" | ||
|
|
||
| tag "bwa/index" | ||
| tag "modules" | ||
| tag "parabricks/fq2bam" | ||
| tag "modules_nfcore" | ||
| tag "parabricks" | ||
|
|
||
| setup { | ||
| run("BWA_INDEX") { | ||
| script "../../../bwa/index/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| run("BWA_INDEX", alias: 'BWA_INDEX_PE') { | ||
| script "../../../bwa/index/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| test("SRR389222 - fastq - se") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:true ], // meta map | ||
| [ | ||
| file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) | ||
| ] | ||
| ]) | ||
| input[1] = Channel.of([ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) | ||
| ]) | ||
| input[2] = BWA_INDEX.out.index | ||
| input[3] = [ [], [] ] | ||
| input[4] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| bam(process.out.bam[0][1]).getReadsMD5(), | ||
| file(process.out.bai[0][1]).name, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("SRR389222 - fastq - se - stub") { | ||
| options '-stub' | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:true ], // meta map | ||
| [ | ||
| file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) | ||
| ] | ||
| ]) | ||
| input[1] = Channel.of([ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) | ||
| ]) | ||
| input[2] = BWA_INDEX.out.index | ||
| input[3] = [ [], [] ] | ||
| input[4] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("sarscov2 - fastq - pe") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ 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([ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ]) | ||
| input[2] = BWA_INDEX_PE.out.index | ||
| input[3] = [ [], [] ] | ||
| input[4] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| bam(process.out.bam[0][1]).getReadsMD5(), | ||
| file(process.out.bai[0][1]).name, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("sarscov2 - fastq - pe - stub") { | ||
| options '-stub' | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ 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([ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ]) | ||
| input[2] = BWA_INDEX_PE.out.index | ||
| input[3] = [ [], [] ] | ||
| input[4] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
Oops, something went wrong.