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Merge pull request #259 from nf-cmgg/merge-fast-processes
Merge fast processes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -43,4 +43,4 @@ template: | |
| skip_features: | ||
| - fastqc | ||
| - is_nfcore | ||
| version: 1.9.3 | ||
| version: 1.10.0dev | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| process BCFTOOLS_FILTER { | ||
| tag "$meta.id" | ||
| label 'process_medium' | ||
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| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': | ||
| 'biocontainers/bcftools:1.20--h8b25389_0' }" | ||
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||
| input: | ||
| tuple val(meta), path(vcf), path(tbi) | ||
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| output: | ||
| tuple val(meta), path("*.${extension}"), emit: vcf | ||
| tuple val(meta), path("*.tbi") , emit: tbi, optional: true | ||
| tuple val(meta), path("*.csi") , emit: csi, 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 args2 = task.ext.args2 ?: '' | ||
| def args3 = task.ext.args3 ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| def last_args = args3 ?: args2 ?: args | ||
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| extension = last_args.contains("--output-type b") || last_args.contains("-Ob") ? "bcf.gz" : | ||
| last_args.contains("--output-type u") || last_args.contains("-Ou") ? "bcf" : | ||
| last_args.contains("--output-type z") || last_args.contains("-Oz") ? "vcf.gz" : | ||
| last_args.contains("--output-type v") || last_args.contains("-Ov") ? "vcf" : | ||
| "vcf" | ||
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| if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" | ||
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| def filter_2 = args2 ? "| bcftools filter --threads ${task.cpus} ${args2}" : "" | ||
| def filter_3 = args3 ? "| bcftools filter --threads ${task.cpus} ${args3}" : "" | ||
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| """ | ||
| bcftools filter \\ | ||
| --threads ${task.cpus} \\ | ||
| $args \\ | ||
| $vcf \\ | ||
| ${filter_2} \\ | ||
| ${filter_3} \\ | ||
| --output ${prefix}.${extension} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') | ||
| END_VERSIONS | ||
| """ | ||
|
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||
| stub: | ||
| def args = task.ext.args ?: '' | ||
| def args2 = task.ext.args2 ?: '' | ||
| def args3 = task.ext.args3 ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
|
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| def last_args = args3 ?: args2 ?: args | ||
|
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| extension = last_args.contains("--output-type b") || last_args.contains("-Ob") ? "bcf.gz" : | ||
| last_args.contains("--output-type u") || last_args.contains("-Ou") ? "bcf" : | ||
| last_args.contains("--output-type z") || last_args.contains("-Oz") ? "vcf.gz" : | ||
| last_args.contains("--output-type v") || last_args.contains("-Ov") ? "vcf" : | ||
| "vcf" | ||
| def index = last_args.contains("--write-index=tbi") || last_args.contains("-W=tbi") ? "tbi" : | ||
| last_args.contains("--write-index=csi") || last_args.contains("-W=csi") ? "csi" : | ||
| last_args.contains("--write-index") || last_args.contains("-W") ? "csi" : | ||
| "" | ||
| def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" | ||
| def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" | ||
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| if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" | ||
|
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| """ | ||
| ${create_cmd} ${prefix}.${extension} | ||
| ${create_index} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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