nf-core_modules/tests/modules/biscuit/mergecg/test.yml
Nathan Spix 801240a971
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

26 lines
1.2 KiB
YAML

- name: biscuit mergecg test_biscuit_mergecg
command: nextflow run tests/modules/biscuit/mergecg -entry test_biscuit_mergecg -c tests/config/nextflow.config
tags:
- biscuit
- biscuit/mergecg
files:
- path: output/biscuit/BiscuitIndex/genome.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
- path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
md5sum: 9c9e07fa1c75ef32d764274579c89b08
- path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
md5sum: 62eb83cd557a47b59589713d98024fc2
- path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
md5sum: 55bcd97d7059bf73dc0d221e36e8e901
- path: output/biscuit/test.bed.gz
md5sum: d693b28ddc81265f388860d391fc7c5b
- path: output/biscuit/versions.yml
md5sum: f670d63671af06bf8654677bf373b3a1