Commits · 37910a095f94d8af17ad11dfed69dd1aaa9c1a0b · zavolan_group / pipelines / ZARP · GitLab

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Jul 16, 2021
- Bump snakemake version that fixes the reported time in snakemake report. · 37910a09
  BIOPZ-Gypas Foivos authored 3 years ago
  
  37910a09
Jul 15, 2021
- Validation of configuration file with a json schema... · 1d3ace6e
  Dominik Burri authored 3 years ago
  1d3ace6e
Jul 14, 2021
- Cutadapt set -m=1 to avoid empty reads · e46e237a
  CJHerrmann authored 3 years ago and Alex Kanitz committed 3 years ago
  
  e46e237a
Jul 13, 2021
- Fix paths to Snakefile for slurm test scripst · 918714cd
  BIOPZ-Gypas Foivos authored 3 years ago
  
  918714cd
Jun 11, 2021
- Add conda support in ZARP · 10885dca
  BIOPZ-Gypas Foivos authored 3 years ago
  
  10885dca
May 07, 2021
- Use biocontainers images for star, gffread, salmon, kallisto, cutadapt,... · be8eb02d
  BIOPZ-Gypas Foivos authored 4 years ago
  be8eb02d
Apr 15, 2021
- feat: enable user to configure CLI params per rule · d35d5500
  CJHerrmann authored 4 years ago and Alex Kanitz committed 4 years ago
  
  d35d5500
Feb 26, 2021
- Remove unnecessary files in the results directory · 6804ea67
  Dominik Burri authored 4 years ago and BIOPZ-Gypas Foivos committed 4 years ago
  
  6804ea67
Feb 11, 2021
- MultiQC plugins for TIN scores and ALFA Fixes #138 · fab75506
  BIOPZ-Bak Maciej authored 4 years ago and BIOPZ-Gypas Foivos committed 4 years ago
  
  fab75506
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
Jun 18, 2020
- Increase memory for salmon index · 595f881e
  BIOPZ-Börsch Anastasiya authored 4 years ago
  
  595f881e
Jun 17, 2020
- Increase memory for some rules · b72a811a
  BIOPZ-Börsch Anastasiya authored 4 years ago
  
  b72a811a
Jun 15, 2020
- fix: Renamed samples_concat.tsv to samples.multiple_lanes.tsv. Renamed rows... · 05c167fd
  BIOPZ-Katsantoni Maria authored 4 years ago and Alex Kanitz committed 4 years ago
  05c167fd
- refactor: rename LabKey/input table column · 82c4dcea
  BIOPZ-Börsch Anastasiya authored 4 years ago and Alex Kanitz committed 4 years ago
  
  82c4dcea
Jun 12, 2020
- Add Snakemake report · f7cda546
  BIOPZ-Bak Maciej authored 4 years ago and Alex Kanitz committed 4 years ago
  
  f7cda546
- fix(prepare_inputs): support relative paths · 402da16e
  Alex Kanitz authored 4 years ago
  
  402da16e
Apr 27, 2020
- Refactor LabKey to Snakemake script · 556f1e12
  Alex Kanitz authored 5 years ago
  556f1e12
- 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
- Update resource requirements for Slurm cluster · aae0ffde
  BIOPZ-Börsch Anastasiya authored 5 years ago and Alex Kanitz committed 5 years ago
  
  aae0ffde
- Fix cutadapt overtrimming · bab8f25a
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  
  bab8f25a
Mar 12, 2020
- add TIN score merge and plot steps · a0babc83
  BIOPZ-Bak Maciej authored 5 years ago
  
  a0babc83
- replaced synthetic test by new one. · 46e6e00b
  Dominik Burri authored 5 years ago
  46e6e00b
- 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
- 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
- handle polyA processing in input preparation script · c4e20a21
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  c4e20a21
Feb 20, 2020
- create log directories in Snakefile\ · 5e1ec85e
  Alex Kanitz authored 5 years ago
  5e1ec85e
Feb 18, 2020
- run tests in verbose mode · 0d95577e
  Alex Kanitz authored 5 years ago
  0d95577e
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