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https://github.com/MillironX/nf-core_modules.git
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50 lines
1.6 KiB
Text
50 lines
1.6 KiB
Text
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process SISTR {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2':
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'quay.io/biocontainers/sistr_cmd:1.1.1--pyh864c0ab_2' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*.tab") , emit: tsv
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tuple val(meta), path("*-allele.fasta"), emit: allele_fasta
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tuple val(meta), path("*-allele.json") , emit: allele_json
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tuple val(meta), path("*-cgmlst.csv") , emit: cgmlst_csv
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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 ?: "${meta.id}"
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def is_compressed = fasta.getName().endsWith(".gz") ? true : false
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def fasta_name = fasta.getName().replace(".gz", "")
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"""
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if [ "$is_compressed" == "true" ]; then
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gzip -c -d $fasta > $fasta_name
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fi
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sistr \\
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--qc \\
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$args \\
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--threads $task.cpus \\
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--alleles-output ${prefix}-allele.json \\
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--novel-alleles ${prefix}-allele.fasta \\
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--cgmlst-profiles ${prefix}-cgmlst.csv \\
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--output-prediction ${prefix} \\
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--output-format tab \\
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$fasta_name
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sistr: \$(echo \$(sistr --version 2>&1) | sed 's/^.*sistr_cmd //; s/ .*\$//' )
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END_VERSIONS
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"""
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}
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