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a6ca2b006b
* add software/cooler * fix the wrong files uploaded. * create a branch for cooler/merge * remove the bin_size from metadata. * update the test_data to test-datasets * update pytest_modules.yml * update the test file from single input file to two input file. update the output file from hdf5 to bedpe. * update the version.txt to version.yml and functions.nf * change version.yml to versions * update the test file path and fix the output versions. * Update meta.yml Correct "version" to "versions" * Update main.nf Fix typo * Update main.nf Remove some spaces Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
41 lines
1.4 KiB
Text
41 lines
1.4 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 COOLER_MERGE {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0"
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} else {
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container "quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0"
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}
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input:
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tuple val(meta), path(cool)
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output:
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tuple val(meta), path("*.cool"), emit: cool
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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cooler merge \\
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$options.args \\
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${prefix}.cool \\
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${cool}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(cooler --version 2>&1 | sed 's/cooler, version //')
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END_VERSIONS
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"""
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}
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