mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
35 lines
1.1 KiB
Text
35 lines
1.1 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
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:[:], 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: gtf
|
|
|
|
script:
|
|
"""
|
|
stringtie \\
|
|
--merge $stringtie_gtf \\
|
|
-G $annotation_gtf \\
|
|
-o stringtie.merged.gtf
|
|
"""
|
|
}
|