Commits · f7ddc28e72bc6ce9a6020e11e190de7c8d1d94fb · center-for-computational-genomics-and-data-science / public / QuaC

Apr 11, 2021
- adds protected tags - #9 · f7ddc28e
  Manavalan Gajapathy authored 3 years ago
  
  f7ddc28e
Apr 09, 2021
- Merge branch 'master' of... · 5670cf16
  Manavalan Gajapathy authored 3 years ago
```
Merge branch 'master' of gitlab.rc.uab.edu:center-for-computational-genomics-and-data-science/sciops/pipelines/quac into qc_under_one_umbrella
```
  5670cf16
- runs indexcov only for input samples - #6 · f184a1ec
  Manavalan Gajapathy authored 3 years ago
  
  f184a1ec
- adds jobname rule to cluster config · a94ba152
  Manavalan Gajapathy authored 3 years ago
  
  a94ba152
- fixes test rename-config files path · 9531c748
  Manavalan Gajapathy authored 3 years ago
  
  9531c748
- adds panoptes monitoring · 2fa49674
  Manavalan Gajapathy authored 3 years ago
  
  2fa49674
- removes sample name prefixing in somalier · f08f4744
  Manavalan Gajapathy authored 3 years ago
  
  f08f4744
- aggregates somalier only for input samples- #6 · c29b603c
  Manavalan Gajapathy authored 3 years ago
  
  c29b603c
- bugfix: mosdepth plot now uses all samples · a1684120
  Manavalan Gajapathy authored 3 years ago
  
  a1684120
- Merge branch 'make_it_production_ready' into 'master' · 00cd5438
  Manavalan Gajapathy authored 3 years ago
```
QuaC - First major review

See merge request center-for-computational-genomics-and-data-science/sciops/pipelines/quac!1
```
  00cd5438
Apr 08, 2021
- bugfix: fixes "units" when aggregating multi-sample qc · e7f36802
  Manavalan Gajapathy authored 3 years ago
  
  e7f36802
- bugfix: changes mosdepth's javascript path · 1ddb554e
  Manavalan Gajapathy authored 3 years ago
  
  1ddb554e
- goes back to older dir structure setup for rename-config · aef2903b
  Manavalan Gajapathy authored 3 years ago
  
  aef2903b
- verifybamid now uses % in qc-checkup · 2e6cd879
  Manavalan Gajapathy authored 3 years ago
  
  2e6cd879
Apr 06, 2021
- raises error if keyword left undefined · 4baf9311
  Manavalan Gajapathy authored 3 years ago
  
  4baf9311
- bugfix: key value · 7847d814
  Manavalan Gajapathy authored 3 years ago
  
  7847d814
- creates multiqc config from template - #12 · b317c78f
  Manavalan Gajapathy authored 3 years ago
  
  b317c78f
- refactors expand · c23f4d68
  Manavalan Gajapathy authored 3 years ago
  
  c23f4d68
- formats by snakefmt · 4fa89fef
  Manavalan Gajapathy authored 3 years ago
  
  4fa89fef
- moves rename config dirpath · 684605d8
  Manavalan Gajapathy authored 3 years ago
  
  684605d8
- updates multiqc config to include bcftools and verifybamid · 739d9e5c
  Manavalan Gajapathy authored 3 years ago
  
  739d9e5c
- switches to uncompressed bed file as capture file reqt · 476f3654
  Manavalan Gajapathy authored 3 years ago
  
  476f3654
- creates multiqc config by templating · fe9136be
  Manavalan Gajapathy authored 3 years ago
  
  fe9136be
- adds exome support to mosdepth · d45e1d9b
  Manavalan Gajapathy authored 3 years ago
  
  d45e1d9b
- adds exome support for qualimap - closes #7 · abd033be
  Manavalan Gajapathy authored 3 years ago
  
  abd033be
- switches to test datasets from na12878 subsampling · 5bfc9f53
  Manavalan Gajapathy authored 3 years ago
  
  5bfc9f53
Apr 03, 2021
- adds docstring · 18ddd9ec
  Manavalan Gajapathy authored 3 years ago
  
  18ddd9ec
- moves the funtction around · 26fd95c2
  Manavalan Gajapathy authored 3 years ago
  
  26fd95c2
- removes unneeded code after refactoring · 31b4255b
  Manavalan Gajapathy authored 3 years ago
  
  31b4255b
- bug fix · 98d73758
  Manavalan Gajapathy authored 3 years ago
  
  98d73758
- generalizes checks that use multiqc general stats file · f73e303b
  Manavalan Gajapathy authored 3 years ago
  
  f73e303b
- updates fastq screen limits; adds bcftools stats limits · 7f4e2f96
  Manavalan Gajapathy authored 3 years ago
  
  7f4e2f96
- quacs verifybamid checkup · d05364a0
  Manavalan Gajapathy authored 3 years ago
  
  d05364a0
- checks mean_cov to median cov ratio in qualimap · 99c25366
  Manavalan Gajapathy authored 3 years ago
  
  99c25366
- updates qualimap expected metrics · bd4dc43f
  Manavalan Gajapathy authored 3 years ago
  
  bd4dc43f
- templates multiqc config · 8926e9a5
  Manavalan Gajapathy authored 3 years ago
  
  8926e9a5
Apr 02, 2021
- bye bye todo · 93f0c4f2
  Manavalan Gajapathy authored 3 years ago
  
  93f0c4f2
- turns off rules.input chaining as it bugs out · e2fdd985
  Manavalan Gajapathy authored 3 years ago
  
  e2fdd985
- determines "units" - closes #8 · 2fb54612
  Manavalan Gajapathy authored 3 years ago
  
  2fb54612
- refactors expand parts for readability · ee22cfff
  Manavalan Gajapathy authored 3 years ago
  
  ee22cfff