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50 lines
2 KiB
Text
50 lines
2 KiB
Text
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process FCS_FCSADAPTOR {
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tag "$meta.id"
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label 'process_low'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the FCS tool. Please use docker or singularity containers."
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}
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-adaptor.0.2.3.sif':
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'ncbi/fcs-adaptor:0.2.3' }"
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input:
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tuple val(meta), path(assembly)
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output:
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tuple val(meta), path("*.cleaned_sequences.fa.gz"), emit: cleaned_assembly
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tuple val(meta), path("*.fcs_adaptor_report.txt") , emit: adaptor_report
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tuple val(meta), path("*.fcs_adaptor.log") , emit: log
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tuple val(meta), path("*.pipeline_args.yaml") , emit: pipeline_args
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tuple val(meta), path("*.skipped_trims.jsonl") , emit: skipped_trims
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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 ?: '--prok' // --prok || --euk
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def prefix = task.ext.prefix ?: "${meta.id}"
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def FCSADAPTOR_VERSION = '0.2.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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/app/fcs/bin/av_screen_x \\
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-o output/ \\
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$args \\
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$assembly
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# compress and/or rename files with prefix
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gzip -cf output/cleaned_sequences/* > "${prefix}.cleaned_sequences.fa.gz"
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cp "output/fcs_adaptor_report.txt" "${prefix}.fcs_adaptor_report.txt"
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cp "output/fcs_adaptor.log" "${prefix}.fcs_adaptor.log"
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cp "output/pipeline_args.yaml" "${prefix}.pipeline_args.yaml"
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cp "output/skipped_trims.jsonl" "${prefix}.skipped_trims.jsonl"
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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FCS-adaptor: $FCSADAPTOR_VERSION
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END_VERSIONS
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"""
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}
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