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

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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 pileup test_biscuit_pileup
command: nextflow run tests/modules/biscuit/pileup -entry test_biscuit_pileup -c tests/config/nextflow.config
tags:
- biscuit
- biscuit/pileup
files:
- path: output/biscuit/BiscuitIndex/genome.fasta
md5sum: f315020d899597c1b57e5fe9f60f4c3e
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
md5sum: 1891c1de381b3a96d4e72f590fde20c1
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
- path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
md5sum: 668799eea40aefb8013cbf8ed6c47cfe
- path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
md5sum: 10541b05bbea44d0344b0345a6522ba8
- path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
md5sum: 2c38edd64234420add133f5fe1ff975d
- path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
md5sum: 7deee1aac3395d93bef1df11ab38379e
- path: output/biscuit/test.vcf.gz
md5sum: ef9798c318ead0f8a79ee7fdeb1ffbf9
- path: output/biscuit/versions.yml
md5sum: ae38b891fdbf9f7ff5c486408f949dc5
- name: biscuit pileup test_biscuit_pileup_somatic
command: nextflow run tests/modules/biscuit/pileup -entry test_biscuit_pileup_somatic -c tests/config/nextflow.config
tags:
- biscuit
- biscuit/pileup
files:
- path: output/biscuit/BiscuitIndex/genome.fasta
md5sum: f315020d899597c1b57e5fe9f60f4c3e
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
md5sum: 1891c1de381b3a96d4e72f590fde20c1
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
- path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
md5sum: 668799eea40aefb8013cbf8ed6c47cfe
- path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
md5sum: 10541b05bbea44d0344b0345a6522ba8
- path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
md5sum: 2c38edd64234420add133f5fe1ff975d
- path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
md5sum: 7deee1aac3395d93bef1df11ab38379e
- path: output/biscuit/test.vcf.gz
md5sum: 692b4a6191b08fabe5efa5abe00da420
- path: output/biscuit/versions.yml
md5sum: cc51fd498d67fdc7cc067686eb855b93
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