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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,83 @@ | ||
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| process GRIDSS_GRIDSS { | ||
| tag "$meta.id" | ||
| label 'process_medium' | ||
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| conda "bioconda::gridss=2.13.2" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h270b39a_0': | ||
| 'biocontainers/gridss:2.13.2--h270b39a_0' }" | ||
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| input: | ||
| tuple val(meta), path(normalbam), path(normalbai), path(tumorbam), path(tumorbai) // required: [meta, normal_cram, normal_crai, tumor_cram, tumor_crai] | ||
| path(fasta) // required: reference fasta | ||
| path(fasta_fai) | ||
| path(bwa_index) // required: bwa index folder | ||
| path(blacklist_gridss) // optional: gridss blacklist bed file based on genome | ||
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| output: | ||
| tuple val(meta), path("*.vcf.gz") , emit: vcf, optional:true | ||
| tuple val(meta), path("*.vcf.gz.tbi") , emit: vcf_index, optional:true | ||
| tuple val(meta), path("*.assembly.bam") , emit: assembly, optional:true | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = '2.13.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| def assembly_bam = "--assembly ${meta.id}.assembly.bam" | ||
| def bwa = bwa_index ? "cp -s ${bwa_index}/* ." : "" | ||
| def blacklist = blacklist_gridss ? "--blacklist ${blacklist_gridss}" : "" | ||
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| """ | ||
| ${bwa} | ||
| gridss \\ | ||
| --output ${prefix}.vcf.gz \\ | ||
| --reference ${fasta} \\ | ||
| --threads ${task.cpus} \\ | ||
| $assembly_bam \\ | ||
| $blacklist \\ | ||
| --picardoptions VALIDATION_STRINGENCY=LENIENT \\ | ||
| --jvmheap ${task.memory.toGiga() - 1}g \\ | ||
| --otherjvmheap ${task.memory.toGiga() - 1}g \\ | ||
| ${normalbam} \\ | ||
| ${tumorbam} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| gridss: ${VERSION} | ||
| END_VERSIONS | ||
| """ | ||
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = '2.13.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
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| def steps = args.contains("-s ") ? args.split('-s ')[-1].split(" ")[0] : | ||
| args.contains("--steps ") ? args.split('--steps ')[-1].split(" ")[0] : | ||
| "all" | ||
| def vcf = steps.contains("call") || steps.contains("all") ? "touch ${prefix}.vcf*" : "" | ||
| def assembly_bam = steps.contains("assembly") || steps.contains("all") ? "touch ${meta.id}.assembly.bam" : "" | ||
| """ | ||
| ${vcf} | ||
| ${assembly_bam} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| gridss: ${VERSION} | ||
| END_VERSIONS | ||
| """ | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| process GRIDSS_SOMATIC { | ||
| tag "$meta.id" | ||
| label 'process_medium' | ||
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| conda "bioconda::gridss=2.13.2" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h270b39a_0': | ||
| 'biocontainers/gridss:2.13.2--h270b39a_0' }" | ||
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| input: | ||
| tuple val(meta), path(gridss_output) | ||
| path(pondir_gridss) | ||
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| output: | ||
| tuple val(meta), path("*high_confidence_somatic.vcf.gz") , emit: somatic_high_vcf, optional:true | ||
| tuple val(meta), path("*high_and_low_confidence_somatic.vcf.gz") , emit: somatic_all_vcf, optional:true | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = '2.13.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| def output1 = "${meta.id}.high_confidence_somatic.vcf.gz" | ||
| def output2 = "${meta.id}.high_and_low_confidence_somatic.vcf.gz" | ||
| //def pon = pondir_gridss ? "cp -s ${pondir_gridss}/* ." : "" | ||
| //def scriptDir = "dirname \$(which gridss_somatic_filter)".execute().text.trim() | ||
| """ | ||
| gridss_somatic_filter \\ | ||
| --pondir ${pondir_gridss} \\ | ||
| --input ${gridss_output} \\ | ||
| --output $output1 \\ | ||
| --fulloutput $output2 \\ | ||
| -n 1 \\ | ||
| -t 2 | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| gridss: ${VERSION} | ||
| END_VERSIONS | ||
| """ | ||
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = '2.13.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| """ | ||
| touch ${prefix}.high_confidence_somatic.vcf.bgz | ||
| touch ${prefix}.high_and_low_confidence_somatic.vcf.bgz | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| gridss: ${VERSION} | ||
| END_VERSIONS | ||
| """ | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,80 @@ | ||
| // | ||
| // GRIDSS SV CALLING | ||
| // | ||
| // | ||
| // | ||
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| include { GRIDSS_GRIDSS } from '../../../modules/local/gridss/gridss/main.nf' | ||
| include { GRIDSS_SOMATIC } from '../../../modules/local/gridss/somaticFilter/main.nf' | ||
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| workflow BAM_SVCALLING_GRIDSS { | ||
| take: | ||
| cram // channel: [mandatory] [ meta, normalcram, normalcrai, tumorcram, tumorcrai ] | ||
| fasta // channel: [mandatory] reference fasta | ||
| fasta_fai // channel: [mandatory] reference fasta index | ||
| bwa_index // channel: [mandatory] bwa index path | ||
| blacklist_gridss // optional: blacklist bed file for gridss | ||
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| main: | ||
| versions = Channel.empty() | ||
| vcf = Channel.empty() | ||
| vcf_index = Channel.empty() | ||
| assembly_bam = Channel.empty() | ||
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| GRIDSS_GRIDSS(cram, fasta, fasta_fai, bwa_index, blacklist_gridss) | ||
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| vcf = GRIDSS_GRIDSS.out.vcf | ||
| vcf_index = GRIDSS_GRIDSS.out.vcf_index | ||
| assembly_bam = GRIDSS_GRIDSS.out.assembly | ||
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| versions = versions.mix(GRIDSS_GRIDSS.out.versions) | ||
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| emit: | ||
| vcf | ||
| vcf_index | ||
| assembly_bam | ||
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| versions | ||
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| } | ||
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| workflow BAM_SVCALLING_GRIDSS_SOMATIC { | ||
| take: | ||
| vcf | ||
| pondir_gridss | ||
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| main: | ||
| versions = Channel.empty() | ||
| somatic_all = Channel.empty() | ||
| somatic_high_confidence = Channel.empty() | ||
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| GRIDSS_SOMATIC(vcf, pondir_gridss) | ||
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| somatic_all = GRIDSS_SOMATIC.out.somatic_all_vcf | ||
| somatic_high_confidence = GRIDSS_SOMATIC.out.somatic_high_vcf | ||
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| versions = GRIDSS_SOMATIC.out.versions | ||
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| all_vcf = Channel.empty().mix(somatic_all, somatic_high_confidence) | ||
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| emit: | ||
| somatic_all | ||
| somatic_high_confidence | ||
| all_vcf | ||
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| versions | ||
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| } | ||
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