2021-05-03 05:18:51 +00:00
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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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2021-07-21 13:38:40 +00:00
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conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
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2021-11-26 07:58:40 +00:00
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
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'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
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2021-05-03 05:18:51 +00:00
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input:
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2021-07-01 15:13:01 +00:00
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path stringtie_gtf
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path annotation_gtf
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2021-05-03 05:18:51 +00:00
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output:
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2021-07-01 15:13:01 +00:00
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path "stringtie.merged.gtf", emit: gtf
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2021-10-01 13:04:56 +00:00
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path "versions.yml" , emit: versions
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2021-05-03 05:18:51 +00:00
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script:
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2021-11-26 07:58:40 +00:00
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def args = task.ext.args ?: ''
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2021-05-03 05:18:51 +00:00
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"""
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stringtie \\
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--merge $stringtie_gtf \\
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-G $annotation_gtf \\
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-o stringtie.merged.gtf
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2021-07-21 13:38:40 +00:00
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2021-09-27 08:41:24 +00:00
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cat <<-END_VERSIONS > versions.yml
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2021-11-26 07:58:40 +00:00
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"${task.process}":
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stringtie: \$(stringtie --version 2>&1)
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2021-09-27 08:41:24 +00:00
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END_VERSIONS
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2021-05-03 05:18:51 +00:00
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"""
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}
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