Commits · 78fccac8f93a518bf5e98a722313e6b0b9fcff67 · zavolan_group / pipelines / ZARP · GitLab

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Mar 19, 2020
- MultiQC · fd1e3123
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  
  fd1e3123
Mar 12, 2020
- add TIN score merge and plot steps · a0babc83
  BIOPZ-Bak Maciej authored 5 years ago
  
  a0babc83
- included tests for ALFA qc · ad3a8e52
  Dominik Burri authored 5 years ago
  ad3a8e52
- added rule for · 37fb0fd0
  Dominik Burri authored 5 years ago
  37fb0fd0
Mar 06, 2020
- Merged paired end and single end rules for star_rpm and... · fb784999
  BIOPZ-Gypas Foivos authored 5 years ago
  fb784999
- 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
- Separate stdout and stderr logs for the majority of rules. Closes #76 and #79 · ff0a39fa
  BIOPZ-Katsantoni Maria authored 5 years ago and BIOPZ-Gypas Foivos committed 5 years ago
  
  ff0a39fa
Feb 24, 2020
- Add rule that combines counts from Salmon · 357ed828
  BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago
  357ed828
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 20, 2020
- create log directories in Snakefile\ · 5e1ec85e
  Alex Kanitz authored 5 years ago
  5e1ec85e
Feb 17, 2020
- add TIN score calculation · c538fe8b
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  c538fe8b
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 14, 2020
- repo follows recommended structure · 1e52fa56
  Alex Kanitz authored 5 years ago
  
  1e52fa56
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
Jan 24, 2020
- update test input files · 4e99b664
  BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago
  4e99b664
Dec 20, 2019
- Rename snakemake/paired_end.snakemake to snakemake/paired_end.snakefile. Fix... · 44d3f3e3
  BIOPZ-Gypas Foivos authored 5 years ago
  44d3f3e3
- Clean up unused code in snakemake/Snakefile. Add 2 threads in htseq_qa (paired... · 5094be70
  BIOPZ-Gypas Foivos authored 5 years ago
  5094be70
- Remove prepare_annotation directory. Rename process_data to snakemake. · cb46aa34
  BIOPZ-Gypas Foivos authored 5 years ago
  
  cb46aa34
Dec 13, 2019
- Started working on subpipelines · cd2052dd
  CJHerrmann authored 5 years ago
  
  cd2052dd
Feb 19, 2019
- Addition of basic steps for process data · 52c1de75
  BIOPZ-Gypas Foivos authored 6 years ago
  
  52c1de75