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bb7beff497
* add hicap module * add info on optional inputs * fix typo * Update meta.yml * Update main.nf * Update meta.yml * Update modules/hicap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/hicap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
56 lines
1.9 KiB
Text
56 lines
1.9 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 HICAP {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::hicap=1.0.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0"
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} else {
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container "quay.io/biocontainers/hicap:1.0.3--py_0"
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}
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input:
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tuple val(meta), path(fasta)
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path database_dir
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path model_fp
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output:
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tuple val(meta), path("*.gbk"), emit: gbk
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tuple val(meta), path("*.svg"), emit: svg
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tuple val(meta), path("*.tsv"), emit: tsv
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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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def database_args = database_dir ? "--database_dir ${database_dir}" : ""
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def model_args = model_fp ? "--model_fp ${model_fp}" : ""
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def is_compressed = fasta.getName().endsWith(".gz") ? true : false
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def fasta_name = fasta.getName().replace(".gz", "")
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"""
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if [ "$is_compressed" == "true" ]; then
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gzip -c -d $fasta > $fasta_name
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fi
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hicap \\
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--query_fp $fasta_name \\
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$database_args \\
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$model_args \\
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$options.args \\
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--threads $task.cpus \\
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-o ./
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$( hicap --version 2>&1 ) | sed 's/^.*hicap //' )
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END_VERSIONS
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"""
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}
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