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https://github.com/MillironX/nf-core_modules.git
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29568f72ca
Added $args to command line and made using a reference annotation optional. Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
46 lines
1.2 KiB
Text
46 lines
1.2 KiB
Text
process STRINGTIE_MERGE {
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label 'process_medium'
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// Note: 2.7X indices incompatible with AWS iGenomes.
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conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
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'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
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input:
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path stringtie_gtf
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path annotation_gtf
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output:
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path "stringtie.merged.gtf", emit: gtf
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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 reference = annotation_gtf ? "-G $annotation_gtf" : ""
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"""
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stringtie \\
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--merge $stringtie_gtf \\
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$reference \\
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-o stringtie.merged.gtf \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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stringtie: \$(stringtie --version 2>&1)
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END_VERSIONS
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"""
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stub:
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"""
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touch stringtie.merged.gtf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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stringtie: \$(stringtie --version 2>&1)
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END_VERSIONS
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"""
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}
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