| - **Pre-processing**: Phasing, QC, variant filtering, variant annotation of the reference panel 
| The preprocessing mode is responsible to the preparation of the multiple input file that will be used by the phasing process. The main processes are :
- **Haplotypes phasing** of the reference panel using [**Shapeit5**](https://odelaneau.github.io/shapeit5/).
- **Filter** the reference panel to select only the necessary variants.
- **Chunking the reference panel** in a subset of region for all the chromosomes.
- **Extract** the positions where to perform the imputation. | +| **Phasing** |
| The phasing mode is the core mode of this pipeline. It is constituted of 3 main steps:
- **Phasing**: Phasing of the target dataset on the reference panel using either:
- [**Glimpse1**](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html)
It's come with the necessety to compute the genotype likelihoods of the target dataset.
This step is done using [BCFTOOLS_mpileup](https://samtools.github.io/bcftools/bcftools.html#mpileup)
- [**Glimpse2**](https://odelaneau.github.io/GLIMPSE/glimpse2/index.html) For this step the reference panel is transformed to binary chunks.
- [**Stitch**](https://github.com/rwdavies/stitch)
- [**Quilt**](https://github.com/rwdavies/QUILT)
- **Ligation**: all the different chunks are merged together.
- **Sampling** (optional) | +| **Simulate** |
| The simulation mode is used to create artificial low informative genetic information from high density data. This allow to compare the imputed result to a _truth_ and therefore evaluate the quality of the imputation. For the moment it is possible to simulate:
- Low-pass data by **downsample** BAM or CRAM using [SAMTOOLS_view -s]() at different depth
- Genotype data by **SNP selecting** the position used by a designated SNP chip.
The simulation mode will also compute the **Genotype likelihoods** of the high density data. | +| **Concordance** |
| This mode compare two vcf together to compute a summary of the differences between them. To do so it use either:
- [**Glimpse1**](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html) concordance process.
- [**Glimpse2**](https://odelaneau.github.io/GLIMPSE/glimpse2/index.html) concordance process
- Or convert the two vcf fill to `.zarr` using [**Scikit allele**](https://scikit-allel.readthedocs.io/en/stable/) and [**anndata**](https://anndata.readthedocs.io/en/latest/) before comparing the SNPs. | +| **Postprocessing** |
| This final process unable to loop the whole pipeline for increasing the performance of the imputation. To do so it filter out the best imputed position and rerun the analysis using this positions. |
+
## Pipeline output
To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/phaseimpute/results) tab on the nf-core website pipeline page.
@@ -80,16 +86,20 @@ For more details about the output files and reports, please refer to the
## Credits
-nf-core/phaseimpute was originally written by LouisLeNezet.
+nf-core/phaseimpute was originally written by Louis Le Nézet.
We thank the following people for their extensive assistance in the development of this pipeline:
-
+- Anabella Trigila
+- Saul Pierotti
+- Eugenia Fontecha
+- Matias Romero Victorica
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+For further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (you can join with [this invite](https://nf-co.re/join/slack)).
For further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citations
@@ -99,6 +109,14 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
+You can cite one of the main imputation methods ([`QUILT`](https://github.com/rwdavies/QUILT)) as follows:
+
+> **Rapid genotype imputation from sequence with reference panels.**
+>
+> Davies, R. W., Kucka, M., Su, D., Shi, S., Flanagan, M., Cunniff, C. M., Chan, Y. F., & Myers, S.
+>
+> _Nature genetics_ 2021 June 03. doi: [10.1038/s41588-021-00877-0](https://doi.org/10.1038/s41588-021-00877-0)
+
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
You can cite the `nf-core` publication as follows:
diff --git a/assets/chr_rename_add.txt b/assets/chr_rename_add.txt
new file mode 100644
index 00000000..c48a2640
--- /dev/null
+++ b/assets/chr_rename_add.txt
@@ -0,0 +1,39 @@
+1 chr1
+2 chr2
+3 chr3
+4 chr4
+5 chr5
+6 chr6
+7 chr7
+8 chr8
+9 chr9
+10 chr10
+11 chr11
+12 chr12
+13 chr13
+14 chr14
+15 chr15
+16 chr16
+17 chr17
+18 chr18
+19 chr19
+20 chr20
+21 chr21
+22 chr22
+23 chr23
+24 chr24
+25 chr25
+26 chr26
+27 chr27
+28 chr28
+29 chr29
+30 chr30
+31 chr31
+32 chr32
+33 chr33
+34 chr34
+35 chr35
+36 chr36
+37 chr37
+38 chr38
+X chrX
diff --git a/assets/chr_rename_del.txt b/assets/chr_rename_del.txt
new file mode 100644
index 00000000..a85016b6
--- /dev/null
+++ b/assets/chr_rename_del.txt
@@ -0,0 +1,39 @@
+chr1 1
+chr2 2
+chr3 3
+chr4 4
+chr5 5
+chr6 6
+chr7 7
+chr8 8
+chr9 9
+chr10 10
+chr11 11
+chr12 12
+chr13 13
+chr14 14
+chr15 15
+chr16 16
+chr17 17
+chr18 18
+chr19 19
+chr20 20
+chr21 21
+chr22 22
+chr23 23
+chr24 24
+chr25 25
+chr26 26
+chr27 27
+chr28 28
+chr29 29
+chr30 30
+chr31 31
+chr32 32
+chr33 33
+chr34 34
+chr35 35
+chr36 36
+chr37 37
+chr38 38
+chr39 X
diff --git a/assets/panel.csv b/assets/panel.csv
new file mode 100644
index 00000000..7286169e
--- /dev/null
+++ b/assets/panel.csv
@@ -0,0 +1,3 @@
+panel,chr,vcf,index
+1000GP,chr21,1000GP_21.vcf,1000GP_21.vcf.csi
+1000GP,chr22,1000GP_22.vcf,1000GP_22.vcf.csi
diff --git a/assets/regionsheet.csv b/assets/regionsheet.csv
new file mode 100644
index 00000000..030c9ba1
--- /dev/null
+++ b/assets/regionsheet.csv
@@ -0,0 +1,2 @@
+chr,start,end
+20,20000000,2200000
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 5f653ab7..217ef7c3 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,bam,bai
+1_BAM_1X,/path/to/.bam,/path/to/.bai
+1_BAM_SNP,/path/to/.bam,/path/to/.bai
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 6a7e788c..971c3fb3 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,7 +1,7 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_input.json",
- "title": "nf-core/phaseimpute pipeline - params.input schema",
+ "title": "nf-core/phaseimpute pipeline - params.input",
"description": "Schema for the file provided with params.input",
"type": "array",
"items": {
@@ -13,21 +13,17 @@
"errorMessage": "Sample name must be provided and cannot contain spaces",
"meta": ["id"]
},
- "fastq_1": {
+ "file": {
"type": "string",
- "format": "file-path",
- "exists": true,
- "pattern": "^\\S+\\.f(ast)?q\\.gz$",
- "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+ "pattern": "^\\S+\\.(bam)|((vcf|bcf)(\\.gz))?$",
+ "errorMessage": "BAM, VCF or BCF file must be provided, cannot contain spaces and must have extension '.bam' or '.vcf', '.bcf' with optional '.gz' extension"
},
- "fastq_2": {
+ "index": {
+ "errorMessage": "Input file index must be provided, cannot contain spaces and must have extension '.bai', '.tbi' or '.csi'",
"type": "string",
- "format": "file-path",
- "exists": true,
- "pattern": "^\\S+\\.f(ast)?q\\.gz$",
- "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+ "pattern": "^\\S+\\.(bai|tbi|csi)$"
}
},
- "required": ["sample", "fastq_1"]
+ "required": ["sample", "file", "index"]
}
}
diff --git a/assets/schema_input_panel.json b/assets/schema_input_panel.json
new file mode 100644
index 00000000..242a4136
--- /dev/null
+++ b/assets/schema_input_panel.json
@@ -0,0 +1,35 @@
+{
+ "$schema": "http://json-schema.org/draft-07/schema",
+ "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_input_panel.json",
+ "title": "nf-core/phaseimpute pipeline - params.panel schema",
+ "description": "Schema for the file provided with params.panel",
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "panel": {
+ "type": "string",
+ "pattern": "^\\S+$",
+ "errorMessage": "Panel name must be provided as a string and cannot contain spaces",
+ "meta": ["id"]
+ },
+ "chr": {
+ "type": "string",
+ "pattern": "^\\S+$",
+ "errorMessage": "Chromosome must be provided as a string and cannot contain spaces",
+ "meta": ["chr"]
+ },
+ "vcf": {
+ "type": "string",
+ "pattern": "^\\S+\\.(vcf|bcf)(.gz)?$",
+ "errorMessage": "Panel file must be provided, cannot contain spaces and must have extension '.vcf' or '.bcf' with optional '.gz' extension"
+ },
+ "index": {
+ "type": "string",
+ "pattern": "^\\S+\\.(vcf|bcf)(\\.gz)?\\.(tbi|csi)$",
+ "errorMessage": "Panel index file must be provided, cannot contain spaces and must have extension '.vcf' or '.bcf' with optional '.gz' extension and with '.csi' or '.tbi' extension"
+ }
+ },
+ "required": ["panel", "chr", "vcf", "index"]
+ }
+}
diff --git a/assets/schema_input_region.json b/assets/schema_input_region.json
new file mode 100644
index 00000000..5592aea9
--- /dev/null
+++ b/assets/schema_input_region.json
@@ -0,0 +1,28 @@
+{
+ "$schema": "http://json-schema.org/draft-07/schema",
+ "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_input_region.json",
+ "title": "nf-core/phaseimpute pipeline - params.input_region schema",
+ "description": "Schema for the file provided with params.input_region",
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "chr": {
+ "type": "string",
+ "pattern": "^\\S+$",
+ "errorMessage": "Chromosome name must be provided as a string and cannot contain spaces"
+ },
+ "start": {
+ "type": "integer",
+ "pattern": "^\\d+$",
+ "errorMessage": "Region start name must be provided, cannot contain spaces and must be numeric"
+ },
+ "end": {
+ "type": "integer",
+ "pattern": "^\\d+$",
+ "errorMessage": "Region end name must be provided, cannot contain spaces and must be numeric"
+ }
+ },
+ "required": ["chr", "start", "end"]
+ }
+}
diff --git a/assets/schema_map.json b/assets/schema_map.json
new file mode 100644
index 00000000..4b981006
--- /dev/null
+++ b/assets/schema_map.json
@@ -0,0 +1,24 @@
+{
+ "$schema": "http://json-schema.org/draft-07/schema",
+ "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_map.json",
+ "title": "nf-core/phaseimpute pipeline - params.map schema",
+ "description": "Schema for the file provided with params.map",
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "chr": {
+ "type": "string",
+ "pattern": "^(chr)?[0-9]+$",
+ "errorMessage": "Chromosome must be provided and must be a string containing only numbers, with or without the prefix 'chr'",
+ "meta": ["chr"]
+ },
+ "map": {
+ "type": "string",
+ "pattern": "^\\S+\\.(g)?map(\\.gz)?$",
+ "errorMessage": "Map file must be provided, cannot contain spaces and must have extension '.map' or '.gmap' with optional 'gz' extension"
+ }
+ },
+ "required": ["chr", "map"]
+ }
+}
diff --git a/assets/schema_posfile.json b/assets/schema_posfile.json
new file mode 100644
index 00000000..5a3c9d5a
--- /dev/null
+++ b/assets/schema_posfile.json
@@ -0,0 +1,24 @@
+{
+ "$schema": "http://json-schema.org/draft-07/schema",
+ "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_posfile.json",
+ "title": "nf-core/phaseimpute pipeline - params.posfile schema",
+ "description": "Schema for the file provided with params.posfile",
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "chr": {
+ "type": "string",
+ "pattern": "^\\S+$",
+ "errorMessage": "Chromosome name must be provided as a string and cannot contain spaces",
+ "meta": ["chr"]
+ },
+ "file": {
+ "type": "string",
+ "pattern": "^\\S+\\.txt$",
+ "errorMessage": "Posfile per chromosome must be provided. Must have .txt extension"
+ }
+ },
+ "required": ["chr", "file"]
+ }
+}
diff --git a/conf/modules.config b/conf/modules.config
index d203d2b6..f212b77c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -18,10 +18,6 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
- withName: FASTQC {
- ext.args = '--quiet'
- }
-
withName: 'MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
@@ -30,5 +26,4 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
-
}
diff --git a/conf/steps/imputation.config b/conf/steps/imputation.config
new file mode 100644
index 00000000..7e859eca
--- /dev/null
+++ b/conf/steps/imputation.config
@@ -0,0 +1,33 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Available keys to override module options:
+ ext.args = Additional arguments appended to command in module.
+ ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
+ ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
+ ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_IMPUT:.*' {
+ publishDir = [
+ path: { "${params.outdir}/imputation/concat" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ ext.prefix = { "${meta.id}_impute_concat" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_IMPUT:BCFTOOLS_CONCAT' {
+ ext.args = {[
+ "--ligate",
+ "--output-type z",
+ ].join(" ").trim()}
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_IMPUT:BCFTOOLS_INDEX' {
+ ext.args = "--tbi"
+ }
+}
diff --git a/conf/steps/imputation_glimpse1.config b/conf/steps/imputation_glimpse1.config
new file mode 100644
index 00000000..521c8beb
--- /dev/null
+++ b/conf/steps/imputation_glimpse1.config
@@ -0,0 +1,106 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Available keys to override module options:
+ ext.args = Additional arguments appended to command in module.
+ ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
+ ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
+ ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+ // Configuration for the glimpse1 imputation subworkflow
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_INPUT:.*' {
+ publishDir = [
+ path: { "${params.outdir}/imputation/glimpse1/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ enabled: false
+ ]
+ }
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_INPUT:BCFTOOLS_MPILEUP' {
+ ext.args = [
+ "-I",
+ "-E",
+ "-a 'FORMAT/DP'"
+ ].join(' ')
+ ext.args2 = [
+ "-Aim",
+ "-C alleles"
+ ].join(' ')
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.call" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_INPUT:BCFTOOLS_ANNOTATE' {
+ ext.args = "--set-id '%CHROM:%POS:%REF:%ALT' -Oz"
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.annotate" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_INPUT:BCFTOOLS_INDEX' {
+ ext.args = "--tbi"
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:.*' {
+ publishDir = [
+ path: { "${params.outdir}/imputation/glimpse1/" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_CHUNK' {
+ ext.args = [
+ "--window-size 200000",
+ "--buffer-size 20000"
+ ].join(' ')
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.chunk" }
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_PHASE' {
+ ext.args = [
+ "--impute-reference-only-variants"
+ ].join(' ')
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.phase" }
+ ext.suffix = "bcf"
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:INDEX_PHASE' {
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_LIGATE' {
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.ligate" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:INDEX_LIGATE' {
+ publishDir = [
+ path: { "${params.outdir}/imputation/glimpse1" }
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:.*' {
+ publishDir = [
+ [
+ path: { "${params.outdir}/imputation/glimpse1/concat" },
+ mode: params.publish_dir_mode,
+ ],
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:BCFTOOLS_CONCAT' {
+ ext.args = {[
+ "--ligate",
+ "--output-type z",
+ ].join(" ").trim()}
+ ext.prefix = { "${meta.id}_glimpse1" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:BCFTOOLS_INDEX' {
+ ext.args = "--tbi"
+ ext.prefix = { "${meta.id}_glimpse1" }
+ }
+}
diff --git a/conf/steps/imputation_quilt.config b/conf/steps/imputation_quilt.config
new file mode 100644
index 00000000..fbb8dcc4
--- /dev/null
+++ b/conf/steps/imputation_quilt.config
@@ -0,0 +1,92 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Available keys to override module options:
+ ext.args = Additional arguments appended to command in module.
+ ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
+ ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
+ ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+ withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+ publishDir = [
+ path: { "${params.outdir}/pipeline_info" },
+ mode: params.publish_dir_mode,
+ pattern: '*_versions.yml'
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:.*' {
+
+ ext.prefix = { "${meta.id}_${meta.chr}" }
+
+ publishDir = [
+ [
+ path: { "${params.outdir}/imputation/quilt/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}_chunk" },
+ mode: params.publish_dir_mode,
+ enabled: false
+ ],
+
+
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:GLIMPSE_CHUNK' {
+ ext.prefix = { "${meta.id}_${meta.chr}" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:.*' {
+ publishDir = [
+ [
+ path: { "${params.outdir}/imputation/quilt/" },
+ mode: params.publish_dir_mode,
+ ],
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:QUILT_QUILT' {
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.impute" }
+ publishDir = [enabled: false]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:BCFTOOLS_INDEX_1' {
+ ext.args = "--tbi"
+ publishDir = [enabled: false]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:BCFTOOLS_ANNOTATE' {
+ ext.args = "--set-id '%CHROM:%POS:%REF:%ALT' -Oz"
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.impute.annotate" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:BCFTOOLS_INDEX_2' {
+ ext.args = "--tbi"
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:.*' {
+ publishDir = [
+ [
+ path: { "${params.outdir}/imputation/quilt/concat" },
+ mode: params.publish_dir_mode,
+ ],
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:BCFTOOLS_CONCAT' {
+ ext.args = {[
+ "--ligate",
+ "--output-type z",
+ ].join(" ").trim()}
+ ext.prefix = { "${meta.id}_quilt" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:BCFTOOLS_INDEX' {
+ ext.args = "--tbi"
+ ext.prefix = { "${meta.id}_quilt" }
+ }
+
+}
diff --git a/conf/steps/imputation_stitch.config b/conf/steps/imputation_stitch.config
new file mode 100644
index 00000000..920255e0
--- /dev/null
+++ b/conf/steps/imputation_stitch.config
@@ -0,0 +1,111 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Available keys to override module options:
+ ext.args = Additional arguments appended to command in module.
+ ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
+ ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
+ ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+ withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+ publishDir = [
+ path: { "${params.outdir}/pipeline_info" },
+ mode: params.publish_dir_mode,
+ pattern: '*_versions.yml'
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:.*' {
+ publishDir = [
+ path: { "${params.outdir}/prep_panel/posfile/" },
+ mode: params.publish_dir_mode,
+ enabled: true
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:GAWK' {
+ ext.args = "'{ key = \$1 FS \$2 } !seen[key]++'"
+ ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" }
+ ext.suffix = ".txt"
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_NORM' {
+ ext.args = '-m +any --output-type z'
+ ext.prefix = { "${meta.id}_${meta.chr}_multiallelic" }
+ maxRetries = 2
+ publishDir = [enabled: false]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_VIEW' {
+ ext.args = '-v snps -Oz'
+ ext.prefix = { "${meta.id}_${meta.chr}_biallelic" }
+ maxRetries = 2
+ publishDir = [enabled: false]
+
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_INDEX' {
+ maxRetries = 2
+ publishDir = [enabled: false]
+
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_INDEX_2' {
+ ext.args = '--tbi'
+ maxRetries = 2
+ publishDir = [enabled: false]
+
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:BCFTOOLS_QUERY' {
+ ext.args = [
+ "-f'%CHROM\t%POS\t%REF\t%ALT\\n'",
+ ].join(' ')
+ ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" }
+ publishDir = [enabled: false]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:.*' {
+ publishDir = [
+ path: { "${params.outdir}/imputation/stitch/" },
+ mode: params.publish_dir_mode,
+ enabled: true
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:BCFTOOLS_INDEX' {
+ ext.args = '--tbi'
+ maxRetries = 2
+ publishDir = [enabled: false]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:.*' {
+ publishDir = [
+ [
+ path: { "${params.outdir}/imputation/stitch/concat" },
+ mode: params.publish_dir_mode,
+ ],
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_CONCAT' {
+ ext.args = {[
+ "--ligate",
+ "--output-type z",
+ ].join(" ").trim()}
+ ext.prefix = { "${meta.id}_stitch" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_INDEX' {
+ ext.args = "--tbi"
+ ext.prefix = { "${meta.id}_stitch" }
+ }
+
+
+
+}
diff --git a/conf/steps/initialisation.config b/conf/steps/initialisation.config
new file mode 100644
index 00000000..7cc8daf5
--- /dev/null
+++ b/conf/steps/initialisation.config
@@ -0,0 +1,21 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Available keys to override module options:
+ ext.args = Additional arguments appended to command in module.
+ ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
+ ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
+ ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+ withName: 'PIPELINE_INITIALISATION:.*' {
+ publishDir = [
+ path: { "${params.outdir}/initialisation/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+ mode: params.publish_dir_mode,
+ enabled: false
+ ]
+ }
+}
diff --git a/conf/steps/panel_prep.config b/conf/steps/panel_prep.config
new file mode 100644
index 00000000..7497e3f0
--- /dev/null
+++ b/conf/steps/panel_prep.config
@@ -0,0 +1,152 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Available keys to override module options:
+ ext.args = Additional arguments appended to command in module.
+ ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
+ ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
+ ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHR_CHECK:.*' {
+ publishDir = [
+ path: { "${params.outdir}/prep_panel/" },
+ mode: params.publish_dir_mode,
+ enabled: false
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHR_CHECK:VCF_CHR_RENAME:BCFTOOLS_ANNOTATE' {
+ ext.args = [
+ "-Oz",
+ "--no-version"
+ ].join(' ')
+ ext.prefix = { "${meta.id}_chrrename" }
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_NORM' {
+ ext.args = '-m +any --no-version --output-type z'
+ ext.prefix = { "${meta.id}_${meta.chr}_multiallelic" }
+ maxRetries = 2
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_INDEX' {
+ ext.args = "--tbi"
+ publishDir = [enabled: false]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_VIEW' {
+ ext.args = '-v snps -Oz'
+ ext.prefix = { "${meta.id}_${meta.chr}_biallelic" }
+ maxRetries = 2
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_INDEX_2' {
+ ext.args = '--tbi'
+ maxRetries = 2
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SITES_EXTRACT_BCFTOOLS:VIEW_VCF_SNPS' {
+ ext.args = [
+ "-m 2",
+ "-M 2",
+ "-v snps",
+ "--output-type z",
+ "--no-version"
+ ].join(' ')
+ ext.prefix = { "${meta.id}_SNPS" }
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SITES_EXTRACT_BCFTOOLS:VIEW_VCF_SITES' {
+ ext.args = [
+ "-G",
+ "-m 2",
+ "-M 2",
+ "-v snps",
+ "--output-type z",
+ "--no-version"
+ ].join(' ')
+ ext.prefix = { "${meta.id}_C${meta.chr}_SITES" }
+ publishDir = [
+ path: { "${params.outdir}/prep_panel/sites/vcf/" },
+ mode: params.publish_dir_mode,
+ enabled: true
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SITES_EXTRACT_BCFTOOLS:BCFTOOLS_QUERY' {
+ ext.args = [
+ "-f'%CHROM\t%POS\t%REF,%ALT\\n'",
+ ].join(' ')
+ ext.prefix = { "${meta.id}_glimpse_SITES_TSV" }
+ publishDir = [
+ path: { "${params.outdir}/prep_panel/sites/tsv/" },
+ mode: params.publish_dir_mode,
+ enabled: true
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SITES_EXTRACT_BCFTOOLS:TABIX_TABIX' {
+ ext.args = [
+ "-s1",
+ "-b2",
+ "-e2"
+ ].join(' ')
+ ext.prefix = { "${meta.id}_glimpse_SITES_TSV" }
+ publishDir = [
+ path: { "${params.outdir}/prep_panel/sites/tsv/" },
+ mode: params.publish_dir_mode,
+ enabled: true
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_CONVERT' {
+ ext.args = {"--haplegendsample ${meta.id}_${meta.chr}"}
+ maxRetries = 2
+ publishDir = [
+ path: { "${params.outdir}/prep_panel/haplegend/" },
+ mode: params.publish_dir_mode,
+ enabled: true
+ ]
+ }
+
+ // Phasing
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_PANEL:VCF_PHASE_SHAPEIT5:BEDTOOLS_MAKEWINDOWS' {
+ ext.args = [
+ '-w 60000',
+ '-s 40000'
+ ].join(' ')
+ ext.prefix = { "${meta.id}_chunks" }
+ publishDir = [ enabled: false ]
+ }
+
+ // TSV
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SITES_EXTRACT_BCFTOOLS:BCFTOOLS_QUERY_STITCH' {
+ ext.args = [
+ "-f'%CHROM\t%POS\t%REF\t%ALT\\n'",
+ ].join(' ')
+ ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" }
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SITES_EXTRACT_BCFTOOLS:GAWK_STITCH' {
+ ext.args = "'{ key = \$1 FS \$2 } !seen[key]++'"
+ ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" }
+ ext.suffix = "txt"
+ publishDir = [
+ path: { "${params.outdir}/prep_panel/sites/tsv/" },
+ mode: params.publish_dir_mode,
+ enabled: true
+ ]
+ }
+
+
+}
diff --git a/conf/steps/simulation.config b/conf/steps/simulation.config
new file mode 100644
index 00000000..412c82a4
--- /dev/null
+++ b/conf/steps/simulation.config
@@ -0,0 +1,44 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Available keys to override module options:
+ ext.args = Additional arguments appended to command in module.
+ ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
+ ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
+ ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_REGION:.*' {
+ publishDir = [
+ path: { "${params.outdir}/simulation/" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ enabled: false
+ ]
+ }
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_REGION:SAMTOOLS_VIEW' {
+ ext.args = [
+ ].join(' ')
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}" }
+ }
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:.*' {
+ publishDir = [
+ path: { "${params.outdir}/simulation/" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ ]
+ }
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_COVERAGE' {
+ ext.args = [
+ ].join(' ')
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.stats" }
+ }
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_VIEW' {
+ ext.args = [
+ ].join(' ')
+ ext.prefix = { "${meta.id}_D${meta.depth}_R${meta.region.replace(':','_')}" }
+ }
+}
diff --git a/conf/steps/validation.config b/conf/steps/validation.config
new file mode 100644
index 00000000..d84d2c63
--- /dev/null
+++ b/conf/steps/validation.config
@@ -0,0 +1,91 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Available keys to override module options:
+ ext.args = Additional arguments appended to command in module.
+ ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
+ ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
+ ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+ // Configuration for the validation step
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:.*' {
+ publishDir = [
+ path: { "${params.outdir}/validation/truth" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ enabled: false
+ ]
+ }
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:BCFTOOLS_MPILEUP' {
+ ext.args = [
+ "-I",
+ "-E",
+ "-a 'FORMAT/DP'"
+ ].join(' ')
+ ext.args2 = [
+ "-Aim",
+ "-C alleles"
+ ].join(' ')
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}_truth.call" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:BCFTOOLS_ANNOTATE' {
+ ext.args = "--set-id '%CHROM:%POS:%REF:%ALT' -Oz"
+ ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.annotate" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:BCFTOOLS_INDEX' {
+ ext.args = "--tbi"
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_TRUTH:.*' {
+ publishDir = [
+ path: { "${params.outdir}/validation/concat" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ ext.prefix = { "${meta.id}_truth_concat" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_TRUTH:BCFTOOLS_CONCAT' {
+ ext.args = {[
+ "--ligate",
+ "--output-type z",
+ ].join(" ").trim()}
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_TRUTH:BCFTOOLS_INDEX' {
+ ext.args = "--tbi"
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:.*' {
+ publishDir = [
+ path: { "${params.outdir}/validation/" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GLIMPSE2_CONCORDANCE' {
+ ext.prefix = { "${meta.id}.concordance" }
+ ext.args = "--out-r2-per-site"
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:CONCATENATE' {
+ ext.suffix = { "txt" }
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GUNZIP' {
+ publishDir = [ enabled: false ]
+ }
+
+ withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:ADD_COLUMNS' {
+ ext.prefix = { "${meta.id}_D${meta.depth}_P${meta.panel}_SNP" }
+ publishDir = [ enabled: false ]
+ }
+}
diff --git a/conf/test.config b/conf/test.config
index 7bd1bf14..8a7e5331 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -16,14 +16,19 @@ params {
// Limit resources so that this can run on GitHub Actions
max_cpus = 2
- max_memory = '6.GB'
- max_time = '6.h'
+ max_memory = '2.GB'
+ max_time = '1.h'
// Input data
- // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
- // TODO nf-core: Give any required params for the test so that command line flags are not needed
- input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+ input = "${projectDir}/tests/csv/sample_bam.csv"
+ input_region = "${projectDir}/tests/csv/region.csv"
// Genome references
- genome = 'R64-1-1'
+ fasta = params.pipelines_testdata_base_path + "reference_genome/21_22/hs38DH.chr21_22.fa"
+ panel = "${projectDir}/tests/csv/panel.csv"
+ phased = true
+
+ // Impute parameters
+ step = "panelprep,impute"
+ tools = "glimpse1"
}
diff --git a/conf/test_all.config b/conf/test_all.config
new file mode 100644
index 00000000..3e95cb32
--- /dev/null
+++ b/conf/test_all.config
@@ -0,0 +1,35 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Defines input files and everything required to run a fast and simple pipeline test.
+
+ Use as follows:
+ nextflow run nf-core/phaseimpute -profile test_all,
-
+### Convert
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
+- `imputation/bcftools/convert/`
+ - `*.hap`: a .hap file for the reference panel.
+ - `*.legend*`: a .legend file for the reference panel.
-
+[bcftools](https://samtools.github.io/bcftools/bcftools.html) aids in the conversion of vcf files to .hap and .legend files. A .samples file is also generated. Once that you have generated the hap and legend files for your reference panel, you can skip the reference preparation step and directly submit these files for imputation (to be developed).
-
+### QUILT
-
+- `imputation/quilt/`
+- `quilt.*.vcf.gz`: Imputed VCF for a specific chunk.
+- `quilt.*.vcf.gz.tbi`: TBI for the Imputed VCF for a specific chunk.
-:::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
+[quilt](https://github.com/rwdavies/QUILT) performs the imputation. This step will contain the VCF for each of the chunks.
+
+### Concat
+
+- `imputation/bcftools/concat`
+- `.*.vcf.gz`: Imputed and ligated VCF for all the input samples.
+
+[bcftools concat](https://samtools.github.io/bcftools/bcftools.html) will produce a single VCF from a list of imputed VCFs in chunks.
+
+## STITCH imputation mode
+
+The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
+
+- [Remove Multiallelics](#multiallelics) - Remove multiallelic sites
+- [STITCH](#quilt) - Perform imputation
+- [Concatenate](#concatenate) - Concatenate all imputed chunks into a single VCF
+
+### Concat
+
+- `imputation/bcftools/concat`
+- `.*.vcf.gz`: Imputed and concatenated VCF for all the input samples.
+
+[bcftools concat](https://samtools.github.io/bcftools/bcftools.html) will produce a single VCF from a list of imputed VCFs.
+
+## Reports
+
+Reports contain useful metrics and pipeline information for the different modes.
+
+- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
### MultiQC
@@ -51,6 +85,7 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
+[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see Output files
+- `imputation/glimpse_chunk/` + - `*.txt`: TXT file containing the chunks obtained from running Glimpse chunks. -- `fastqc/` - - `*_fastqc.html`: FastQC report containing quality metrics. - - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. +[Glimpse chunk](https://odelaneau.github.io/GLIMPSE/) defines chunks where to run imputation. For further reading and documentation see the [Glimpse documentation](https://odelaneau.github.io/GLIMPSE/glimpse1/commands.html). Once that you have generated the chunks for your reference panel, you can skip the reference preparation step and directly submit this file for imputation. -| Process Name | +Software | +Version | +
|---|---|---|
| {process if (i == 0) else ''} | +{tool} | +{version} | +
| Process Name | \\n\\", + " \\ Software | \\nVersion | \\n
|---|---|---|
| CUSTOM_DUMPSOFTWAREVERSIONS | \\npython | \\n\\", + " \\3.11.7 | \\n
| \\n \\", + " \\ | yaml | \\n5.4.1 | \\n
| TOOL1 | \\ntool1 | \\n\\", + " \\0.11.9 | \\n
| TOOL2 | \\n\\", + " \\tool2 | \\n1.9 | \\n
| Workflow | \\nNextflow | \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] + ], + "timestamp": "2024-01-09T23:01:18.710682" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index ee5507e0..00000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index 70edae4d..00000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,212 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - 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) ] - ]) - """ - } - } - - 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:|
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls | |
| File type | Conventional base calls |