nf-core_modules/modules/stringtie/merge/main.nf
Harshil Patel 6d88f2da8c
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546)
* 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>
2022-04-22 15:13:06 +01:00

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process STRINGTIE_MERGE {
label 'process_medium'
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
input:
path stringtie_gtf
path annotation_gtf
output:
path "stringtie.merged.gtf", emit: gtf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
stringtie \\
--merge $stringtie_gtf \\
-G $annotation_gtf \\
-o stringtie.merged.gtf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
stringtie: \$(stringtie --version 2>&1)
END_VERSIONS
"""
}