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6927f1d086
* new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new snpsites module * new snpsites module * new snpsites module * new snpsites module * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * use sars-cov-2 alignment * remove old test alignment * new snpsites module * new snpsites module * new snpsites module * updated test file names * new snpsites module * revert to gubbins test on upstream * add new lines * renove whitespace * Apply suggestions from code review Co-authored-by: avantonder <avt@sanger.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: avantonder <ajv37@cam.ac.uk>
39 lines
1.2 KiB
Text
39 lines
1.2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process SNPSITES {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0"
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} else {
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container "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
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}
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input:
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path alignment
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output:
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path "*.fas" , emit: fasta
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path "*.sites.txt" , emit: constant_sites
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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snp-sites -c \\
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$alignment \\
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> filtered_alignment.fas
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echo \$(snp-sites -C $alignment) > constant.sites.txt
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echo \$(snp-sites -V 2>&1) | sed 's/snp-sites //' > ${software}.version.txt
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"""
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}
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