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e971f538a9
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Fix IQ tree * Fix picard markdup and merge sam * Fix plink/vcf version * Fix plink version output * Fix prokka version command * Fix pydamage * Try fixing markduplicates * Fix snpEff * Fix vcftools version * Fix pydamage and filtersamreads test run * Fix MarkDuplicates tests * Add missing unsorted checks * Remove MD5 sym due to stochasicity in BAM file
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process IQTREE {
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tag "$alignment"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0"
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} else {
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container "quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0"
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}
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input:
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path alignment
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val constant_sites
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output:
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path "*.treefile", emit: phylogeny
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path "versions.yml" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def fconst_args = constant_sites ? "-fconst $constant_sites" : ''
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def memory = task.memory.toString().replaceAll(' ', '')
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"""
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iqtree \\
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$fconst_args \\
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$options.args \\
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-s $alignment \\
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-nt AUTO \\
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-ntmax $task.cpus \\
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-mem $memory \\
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
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END_VERSIONS
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"""
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}
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