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48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
process HICAP {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' :
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'quay.io/biocontainers/hicap:1.0.3--py_0' }"
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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, optional: true
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tuple val(meta), path("*.svg"), emit: svg, optional: true
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tuple val(meta), path("*.tsv"), emit: tsv, optional: true
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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 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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$model_args \\
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$args \\
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--threads $task.cpus \\
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-o ./
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hicap: \$( 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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