nf-core_modules/tests/modules/biscuit/vcf2bed/nextflow.config

process {

    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

}
Add core Biscuit tools (#1354) * create files with nf-core command * update meta.yml files * starting to work on index main.nf * prelim test for index * index test working; not finding all output files * index passing tests * index and align passing tests * prototyping biscuitblaster and pileup * update containers * updates to pileup * pileup passing tests * template creation for more biscuit tools * tests passing on blaster,bsconv,pupsom * epiread passing tests, but need to update SNP bed file path * vcf2bed working; change test file * all biscuit commands passing tests * biscuitblaster rename * try to fix permissions * more permission fixes * trying a couple more permission changes * hopefully last permission fixes * really last permission changes * few more permissions * add when blocks * Remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * changes for first round of review * update meta.yml with more specific links * Update modules/biscuit/biscuitblaster/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Apply new version reporting Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/pileup/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update main.nf * Update modules/biscuit/pileupsomatic/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * update test file path * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * tests passing again * Update modules/biscuit/align/main.nf * Update modules/biscuit/bsconv/main.nf * Update modules/biscuit/epiread/main.nf * Update modules/biscuit/index/main.nf * Update test.yml * Update modules/biscuit/pileupsomatic/main.nf * remove module-specific extension/prefix * remove module-specific extension/prefix * add missing args * switch pileup strategy * update test.yml * remove debug * whitespace cleanup * add in newline escapes * requested changes * Update modules/biscuit/pileup/meta.yml Co-authored-by: Spix <nathan.spix@submit.cm.cluster> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Spix <nathan.spix@node107.cm.cluster> Co-authored-by: njspix <nathan.spix@vai.org> 2022-03-14 09:34:22 -04:00			`process {`

			`publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }`

			`}`