Commits · 79c3d9fded725446294754f15f45dcae67f6a05c · zavolan_group / pipelines / ZARP

Oct 23, 2020
- add --no-hooks for CI tests, mark output files of salmon for multiqc, adjust files for md5 check. · e791ce60
  Dominik Burri authored 4 years ago
  
  e791ce60
Jun 23, 2020
- Merge kallisto rules: kallisto_merge_genes and kallisto_merge_transcript · 1f007e19
  BIOPZ-Iborra de Toledo Paula authored 4 years ago and BIOPZ-Gypas Foivos committed 4 years ago
  1f007e19
Apr 27, 2020
- Major refactoring · 6cf28511
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  6cf28511
- Add rules for bigWig creation · 907082c3
  CJHerrmann authored 5 years ago and Alex Kanitz committed 5 years ago
  
  907082c3
Mar 25, 2020
- Update salmon transcriptome index generation · 4e3cac05
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  
  4e3cac05
Mar 20, 2020
- extend ALFA functionality · f5e2f6ac
  Dominik Burri authored 5 years ago and Alex Kanitz committed 5 years ago
  f5e2f6ac
- Fix Poly(A)-trimming rule · 392b04d2
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  392b04d2
Mar 19, 2020
- MultiQC · fd1e3123
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  
  fd1e3123
Mar 17, 2020
- Fix cutadapt overtrimming · bab8f25a
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  
  bab8f25a
Mar 12, 2020
- included tests for ALFA qc · ad3a8e52
  Dominik Burri authored 5 years ago
  ad3a8e52
Mar 06, 2020
- Replace cufflinks image with gffread image · c3d15275
  BIOPZ-Gypas Foivos authored 5 years ago
  
  c3d15275
- Generate bedgraph file of normalised coverage. Fixes #45 · a54ff3e8
  Dominik Burri authored 5 years ago and BIOPZ-Gypas Foivos committed 5 years ago
  
  a54ff3e8
- Extract transcript sequences from genome (fasta file) and gene annotations (gtf file). Fixes #62 · 0def7b72
  BIOPZ-Iborra de Toledo Paula authored 5 years ago and BIOPZ-Gypas Foivos committed 5 years ago
  
  0def7b72
Feb 21, 2020
- Use minified docker images · dc2afcf9
  Alex Kanitz authored 5 years ago
  
  dc2afcf9
- Add rule that combines TPM values from Salmon · bb1f9b8f
  BIOPZ-Iborra de Toledo Paula authored 5 years ago and Alex Kanitz committed 5 years ago
  bb1f9b8f
Feb 15, 2020
- get Snakemake input from LabKey API · eea0206f
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  eea0206f
Feb 09, 2020
- replace test files with small synthetic ones · 48e012a0
  Alex Kanitz authored 5 years ago
  48e012a0
Feb 08, 2020
- integrate completed rules into workflow · ca9a2bb4
  BIOPZ-Iborra de Toledo Paula authored 5 years ago and Alex Kanitz committed 5 years ago
  ca9a2bb4
Feb 07, 2020
- fix various small issues · 17818f4a
  Alex Kanitz authored 5 years ago
  17818f4a
Feb 04, 2020
- clean up tests · 6a231363
  Alex Kanitz authored 5 years ago
  6a231363