nf-core_modules/tests/modules/biscuit/vcf2bed/test.yml

- name: biscuit vcf2bed test_biscuit_vcf2bed
  command: nextflow run tests/modules/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c tests/config/nextflow.config
  tags:
    - biscuit/vcf2bed
    - biscuit
  files:
    - path: output/biscuit/test.bed.gz
      md5sum: e2dd492289dc8463f364285e31b9553a
    - path: output/biscuit/versions.yml
      md5sum: cd784276e2fb6739d55e1b60d12202cd
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 13:34:22 +00:00			`- name: biscuit vcf2bed test_biscuit_vcf2bed`
			`command: nextflow run tests/modules/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c tests/config/nextflow.config`
			`tags:`
			`- biscuit/vcf2bed`
			`- biscuit`
			`files:`
			`- path: output/biscuit/test.bed.gz`
			`md5sum: e2dd492289dc8463f364285e31b9553a`
			`- path: output/biscuit/versions.yml`
			`md5sum: cd784276e2fb6739d55e1b60d12202cd`