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6d88f2da8c
* Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
34 lines
965 B
Text
34 lines
965 B
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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"""
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stringtie \\
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--merge $stringtie_gtf \\
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-G $annotation_gtf \\
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-o stringtie.merged.gtf
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cat <<-END_VERSIONS > versions.yml
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"${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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