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nf-core_modules/tests/modules/biscuit/epiread/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 epiread test_biscuit_epiread_nosnp
command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_nosnp -c tests/config/nextflow.config
tags:
- biscuit
- biscuit/epiread
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: dbb30b59f4ef6fdfdee38630225c0574
- path: output/biscuit/versions.yml
md5sum: 674a77ac5ca8f4b42d30e58e30c3a9af
- name: biscuit epiread test_biscuit_epiread_snp
command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_snp -c tests/config/nextflow.config
tags:
- biscuit
- biscuit/epiread
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: a29fea6ad74453ec94f8220747dab906
- path: output/biscuit/versions.yml
md5sum: f2f7c4ff3c6a135b1c8a3aff24a44d81
- name: biscuit epiread test_biscuit_epiread_snp_decompress
command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_snp_decompress -c tests/config/nextflow.config
tags:
- biscuit
- biscuit/epiread
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: a29fea6ad74453ec94f8220747dab906
- path: output/biscuit/versions.yml
md5sum: cb0258ebf4e1a731a4310ec17c3dc442
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