MuTect2 Module #153
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| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "YOUR-TOOL=HERE" |
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| process MUTECT2 { | ||
| tag "$meta.id" | ||
| label 'process_high' | ||
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| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': | ||
| 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" | ||
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| input: | ||
| tuple val(meta), path(case_bam), path(control_bam), path(case_bai), path(control_bai) | ||
| tuple path(bed_file), path(fasta_file), path(fasta_index_file), path(fasta_dict_file) | ||
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| output: | ||
| tuple val(meta), path("*.mutect2.vcf"), emit: mutect2_vcf | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def args2 = task.ext.args2 ?: '' | ||
| def case_sample_name = task.ext.prefix ?: "${meta.case_id}" | ||
| def control_sample_name = task.ext.prefix ?: "${meta.control_id}" | ||
| def bed_file = bed_file ? "--intervals ${bed_file}" : '' | ||
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| """ | ||
| gatk "Mutect2" \\ | ||
|
There was a problem hiding this comment. Might be good to add in an arg here so we can add java options. In tempo we set the Xmx for example so it may be good to add a ${jvmarg} here or something. This is how it looks in our Tempo Module. |
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| -R ${fasta_file} \\ | ||
| -I ${case_bam} \\ | ||
| -I ${control_bam} \\ | ||
| -tumor ${case_sample_name} \\ | ||
| -normal ${control_sample_name} \\ | ||
| ${args} \\ | ||
| --output ${meta.id}.mutect2.vcf | ||
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| """ | ||
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| stub: | ||
| """ | ||
| touch ${meta.id}.mutect2.vcf | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| gatk "Mutect2": \$(gatk "Mutect2" --version | sed -e "s/gatk "Mutect2" v//g") | ||
| END_VERSIONS | ||
| """ | ||
| } | ||
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| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "mutect2" | ||
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| description: | ||
| This module wraps GATK 4.5.0 MuTect2 software, which generates VCF files | ||
| and standard output from case-control sample BAM files, BED file coordinates, and | ||
| a reference fasta. | ||
| keywords: | ||
| - vcf | ||
| - case-control | ||
| - bams | ||
| tools: | ||
| - "mutect2": | ||
| description: | ||
| "Generates MuTect2 VCF file and standard output for case-control | ||
| sample BAM files." | ||
| homepage: "https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2" | ||
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| identifier: "" | ||
| input: | ||
| # Only when we have meta | ||
| - - meta: | ||
| type: map | ||
| description: | ||
| Groovy Map containing sample information e.g. `[ tumor_id:'tumor_sample', | ||
| normal_id:'normal_sample' ]` | ||
| - case_bam: | ||
| type: file | ||
| description: Case sample BAM file | ||
| pattern: "*.{bam}" | ||
| - control_bam: | ||
| type: file | ||
| description: Control sample BAM file | ||
| pattern: "*.{bam}" | ||
| - case_bai: | ||
| type: file | ||
| description: Case sample BAM index file | ||
| pattern: "*.{bai}" | ||
| - control_bai: | ||
| type: file | ||
| description: Control sample BAM index file | ||
| pattern: "*.{bai}" | ||
| - - bed_file: | ||
| type: file | ||
| description: Input BED file | ||
| pattern: "*.{bed}" | ||
| - fasta_file: | ||
| type: file | ||
| description: Input reference fasta file | ||
| pattern: "*.{fasta}" | ||
| - fasta_index_file: | ||
| type: list | ||
| description: Input reference fasta index file | ||
| pattern: "*.{fasta.fai}" | ||
| - fasta_dict_file: | ||
| type: file | ||
| description: Input reference fasta dictionary file | ||
| pattern: "*.{dict}" | ||
| output: | ||
| #Only when we have meta | ||
| - mutect2_vcf: | ||
| - meta: | ||
| type: map | ||
| description: Output meta map | ||
| - "*.mutect2.vcf": | ||
| type: file | ||
| description: Output MuTect2 generated VCF file | ||
| authors: | ||
| - "@rnaidu" | ||
| maintainers: | ||
| - "@rnaidu" |
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| nextflow_process { | ||
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| name "Test Process MUTECT2" | ||
| script "../main.nf" | ||
| process "MUTECT2" | ||
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| tag "modules" | ||
| tag "modules_msk" | ||
| tag "mutect2" | ||
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| test("mutect2 - test - vcf") { | ||
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| when { | ||
| process { | ||
| """ | ||
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| input[0] = [ | ||
| [id: 'test', case_id: 'tumor',control_id: 'normal'], | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) | ||
| ] | ||
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| input[1] = [ | ||
| file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) | ||
| ] | ||
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| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success } | ||
| ) | ||
| } | ||
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| } | ||
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| test("mutect2 - vcf - stub") { | ||
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| options "-stub" | ||
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| when { | ||
| process { | ||
| """ | ||
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| input[0] = [ | ||
| [id: 'test', case_id: 'tumor',control_id: 'normal'], | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) | ||
| ] | ||
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| input[1] = [ | ||
| file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true), | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) | ||
| ] | ||
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| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success } | ||
| ) | ||
| } | ||
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| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| mutect2: | ||
| - "modules/msk/mutect2/**" |
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I think you're missing the
tag.ymlandmain.nf.test.snapfiles. You might want to double check some other parts of the nf-test. This might be why the testing and linting aren't running properly?