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Merge pull request #2 from TRON-Bioinformatics/migrate-dsl2
Migrate to DSL 2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| params.memory_mutect2 = "16g" | ||
| params.cpus_mutect2 = 2 | ||
| params.output = 'output' | ||
| params.gnomad = false | ||
| params.pon = false | ||
| params.disable_common_germline_filter = false | ||
| params.reference = false | ||
| params.intervals = false | ||
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| process MUTECT2 { | ||
| cpus params.cpus_mutect2 | ||
| memory params.memory_mutect2 | ||
| tag "${name}" | ||
| publishDir "${params.output}/${name}", mode: "copy" | ||
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| conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) | ||
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| input: | ||
| tuple val(name), val(tumor_bam), val(normal_bam) | ||
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| output: | ||
| tuple val("${name}"), file("${name}.mutect2.unfiltered.vcf"), file("${name}.mutect2.unfiltered.vcf.stats"), emit: unfiltered_vcfs | ||
| tuple val("${name}"), file("${name}.f1r2.tar.gz"), emit: f1r2_stats | ||
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| script: | ||
| normal_panel_option = params.pon ? "--panel-of-normals ${params.pon}" : "" | ||
| germline_filter = params.disable_common_germline_filter ? "" : "--germline-resource ${params.gnomad}" | ||
| normal_inputs = normal_bam.split(",").collect({v -> "--input $v"}).join(" ") | ||
| tumor_inputs = tumor_bam.split(",").collect({v -> "--input $v"}).join(" ") | ||
| intervals_option = params.intervals ? "--intervals ${params.intervals}" : "" | ||
| """ | ||
| gatk --java-options '-Xmx${params.memory_mutect2}' Mutect2 \ | ||
| --reference ${params.reference} \ | ||
| ${intervals_option} \ | ||
| ${germline_filter} \ | ||
| ${normal_panel_option} \ | ||
| ${normal_inputs} --normal-sample normal \ | ||
| ${tumor_inputs} --tumor-sample tumor \ | ||
| --output ${name}.mutect2.unfiltered.vcf \ | ||
| --f1r2-tar-gz ${name}.f1r2.tar.gz | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| params.memory_read_orientation = "16g" | ||
| params.cpus_read_orientation = 2 | ||
| params.output = 'output' | ||
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| process LEARN_READ_ORIENTATION_MODEL { | ||
| cpus params.cpus_read_orientation | ||
| memory params.memory_read_orientation | ||
| tag "${name}" | ||
| publishDir "${params.output}/${name}", mode: "copy" | ||
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| conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) | ||
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| input: | ||
| tuple val(name), file(f1r2_stats) | ||
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| output: | ||
| tuple val(name), file("${name}.read-orientation-model.tar.gz"), emit: read_orientation_model | ||
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| """ | ||
| gatk --java-options '-Xmx${params.memory_read_orientation}' LearnReadOrientationModel \ | ||
| --input ${f1r2_stats} \ | ||
| --output ${name}.read-orientation-model.tar.gz | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| params.memory_pileup = "32g" | ||
| params.cpus_pileup = 2 | ||
| params.output = 'output' | ||
| params.gnomad = false | ||
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| process PILEUP_SUMMARIES { | ||
| cpus params.cpus_pileup | ||
| memory params.memory_pileup | ||
| tag "${name}" | ||
| publishDir "${params.output}/${name}", mode: "copy" | ||
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| conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) | ||
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| input: | ||
| tuple val(name), val(tumor_bam), val(normal_bam) | ||
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| output: | ||
| tuple val("${name}"), file("${name}.pileupsummaries.table"), emit: pileupsummaries | ||
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| script: | ||
| tumor_inputs = tumor_bam.split(",").collect({v -> "--input $v"}).join(" ") | ||
| """ | ||
| gatk --java-options '-Xmx${params.memory_pileup}' GetPileupSummaries \ | ||
| --intervals ${params.gnomad} \ | ||
| --variant ${params.gnomad} \ | ||
| ${tumor_inputs} \ | ||
| --output ${name}.pileupsummaries.table | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| params.memory_contamination = "16g" | ||
| params.cpus_contamination = 2 | ||
| params.output = 'output' | ||
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| process CALCULATE_CONTAMINATION { | ||
| cpus params.cpus_contamination | ||
| memory params.memory_contamination | ||
| tag "${name}" | ||
| publishDir "${params.output}/${name}", mode: "copy" | ||
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| conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) | ||
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| input: | ||
| tuple val(name), file(table) | ||
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| output: | ||
| tuple val(name), file("${name}.segments.table"), file("${name}.calculatecontamination.table"), emit: contaminationTables | ||
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| """ | ||
| gatk --java-options '-Xmx${params.memory_contamination}' CalculateContamination \ | ||
| --input ${table} \ | ||
| -tumor-segmentation ${name}.segments.table \ | ||
| --output ${name}.calculatecontamination.table | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| params.memory_filter = "16g" | ||
| params.cpus_filter = 2 | ||
| params.output = 'output' | ||
| params.reference = false | ||
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| process FILTER_CALLS { | ||
| cpus params.cpus_filter | ||
| memory params.memory_filter | ||
| tag "${name}" | ||
| publishDir "${params.output}/${name}", mode: "copy" | ||
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| conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) | ||
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| input: | ||
| tuple val(name), file(segments_table), file(contamination_table), file(model), file(unfiltered_vcf), file(vcf_stats) | ||
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| output: | ||
| tuple val(name), val("${params.output}/${name}/${name}.mutect2.vcf"), emit: final_vcfs | ||
| file "${name}.mutect2.vcf" | ||
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| """ | ||
| gatk --java-options '-Xmx${params.memory_filter}' FilterMutectCalls \ | ||
| -V ${unfiltered_vcf} \ | ||
| --reference ${params.reference} \ | ||
| --tumor-segmentation ${segments_table} \ | ||
| --contamination-table ${contamination_table} \ | ||
| --ob-priors ${model} \ | ||
| --output ${name}.mutect2.vcf | ||
| """ | ||
| } |
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