mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
47cc7a77bf
* add stub for stringtie * add ballgown file to test.yml * add ballgown file to test.yml forward
44 lines
1.1 KiB
Text
44 lines
1.1 KiB
Text
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
|
|
"""
|
|
|
|
stub:
|
|
"""
|
|
touch stringtie.merged.gtf
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
stringtie: \$(stringtie --version 2>&1)
|
|
END_VERSIONS
|
|
"""
|
|
}
|