nf-core_modules/software/stringtie/merge/main.nf
Yuk Kei Wan 6ad50f8ec4
Add stringtie merge module (from nanoseq modules) (#475)
* add stringtie merge module

* add md5sum and path for stringtie.merged.gtf

* fix errors

* try fixing stringtie check error

* add tag

* remove unreproducible md5sum

* address PR suggestions

* hopefully fix linting error
2021-05-03 07:18:51 +02:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process STRINGTIE_MERGE {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['']) }
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
} else {
container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
}
input:
path stringtie_gtf
path annotation_gtf
output:
path "stringtie.merged.gtf" , emit: merged_gtf
script:
"""
stringtie \\
--merge $stringtie_gtf \\
-G $annotation_gtf \\
-o stringtie.merged.gtf
"""
}