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60 lines
1.8 KiB
Plaintext
60 lines
1.8 KiB
Plaintext
process FALCO {
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tag "$meta.id"
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label 'process_single'
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conda "bioconda::falco=1.2.1"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3':
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'quay.io/biocontainers/falco:1.2.1--h867801b_3' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.html"), emit: html
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tuple val(meta), path("*.txt") , emit: txt
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if ( reads.toList().size() == 1 ) {
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"""
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falco $args --threads $task.cpus ${reads} -D ${prefix}_data.txt -S ${prefix}_summary.txt -R ${prefix}_report.html
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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falco:\$( falco --version | sed -e "s/falco//g" )
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END_VERSIONS
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"""
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} else {
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"""
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[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
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falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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falco:\$( falco --version | sed -e "s/falco//g" )
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END_VERSIONS
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"""
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}
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_data.txt
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touch ${prefix}_fastqc_data.html
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touch ${prefix}_summary.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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falco: \$( falco --version | sed -e "s/falco v//g" )
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END_VERSIONS
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"""
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}
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