nf-core_modules/tests/modules/bwamem2/mem/nextflow.config
Maxime U. Garcia 1765225042
Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125)
* feat: view is now in args2 so we can use sort

* forgot one split_cpus

* feat: update with new logic

* fix: add more info

* fix: remove split_cpus logic
2021-12-08 14:31:27 +00:00

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: BWAMEM2_MEM {
ext.args2 = { sort_bam ? "" : "-bh" }
}
}