Commits · 435af71915e71d41d603070e0fe25792dbffac03 · Christian Arnold / ATACSeq_Snakemake

May 17, 2022
- Fixed typo · 435af719
  Christian Arnold authored 2 years ago
  
  435af719
May 09, 2022
- Fixed an issue with CIP-seq when no control files were given · 37349390
  Christian Arnold authored 2 years ago
  
  37349390
- Fixed an issue where the annotation rule fails for edge cases where the peak file is empty · f31381e0
  Christian Arnold authored 2 years ago
  
  f31381e0
- removed groups, they seem to cause additional /scratch caching issues. Removed... · db3ebb78
  Christian Arnold authored 2 years ago
  
  removed groups, they seem to cause additional /scratch caching issues. Removed until resolved what causes this
  db3ebb78
- Fixed a bug for single-end data that causes the stats rule to fail · 078b3f7c
  Christian Arnold authored 2 years ago
  
  078b3f7c
Apr 28, 2022
- Changed the default for restart times: Set to 1 by default now · 50bc56b8
  Christian Arnold authored 2 years ago
  
  50bc56b8
- Bugfixes · 9a0221cb
  Christian Arnold authored 2 years ago
  
  9a0221cb
- Reversed change from yesterday, scripts section was accidentally removed · ec6fcff5
  Christian Arnold authored 2 years ago
  
  ec6fcff5
Apr 27, 2022
- Removed empty and obselete scripts: parameter from configs · f03f616a
  Christian Arnold authored 2 years ago
  
  f03f616a
- Modified the snakefile to make sure that a local copy should be used · 01e234ae
  Christian Arnold authored 2 years ago
  
  01e234ae
Feb 28, 2022
- Added fix for analyses with just 1 sample & param.sh snakefile clarifications · 58dd8a22
  Christian Arnold authored 3 years ago
  
  58dd8a22
Feb 24, 2022
- Updated snakemake version to 6.4.0 due to workflow.source_path · e50bd6f3
  Christian Arnold authored 3 years ago
  
  e50bd6f3
Feb 23, 2022
- Merge branch 'dev' · 1ee63bfe
  Christian Arnold authored 3 years ago
  
  Updated stable version, after extensive testing and optimization
  1ee63bfe
- Small changes in README · 20f5f4a3
  Christian Arnold authored 3 years ago
  
  20f5f4a3
- Small reorganization and removal of picard command line argument · 09d80332
  Christian Arnold authored 3 years ago
  
  09d80332
- Changed path to Snakefile · a285ff88
  Christian Arnold authored 3 years ago
  
  a285ff88
- Singularity changes · 19a85189
  Christian Arnold authored 3 years ago
  
  19a85189
Feb 22, 2022
- Update README.md · bae122dd
  Christian Arnold authored 3 years ago
  
  bae122dd
- Update README.md · e594eeb6
  Christian Arnold authored 3 years ago
  
  e594eeb6
- New version, major update · af30604f
  Christian Arnold authored 3 years ago
  
  af30604f
- Updated README · d60dcf0f
  Christian Arnold authored 3 years ago
  
  d60dcf0f
- Cleanup · 81b32ed1
  Christian Arnold authored 3 years ago
  
  81b32ed1
- Major update, preparing new ATAC-Seq pipeline version · 57f635d7
  Christian Arnold authored 3 years ago
  
  57f635d7
Jan 11, 2022
- Dev: Intermediate updates · 1f5ab69c
  Christian Arnold authored 3 years ago
  
  1f5ab69c
- Dev: Updated configuration files · 890fe52a
  Christian Arnold authored 3 years ago
  
  890fe52a
Jan 10, 2022
- edited consensus peak script to exclude control samples · a5896961
  Rim Moussa authored 3 years ago
  
  a5896961
- chipseq changes · 1e28aa2d
  Rim Moussa authored 3 years ago
  
  1e28aa2d
Nov 30, 2021
- Bugfixes and additions for dev version · 68bd84f5
  Christian Arnold authored 3 years ago
  
  68bd84f5
Nov 25, 2021
- Added examples/dev/input to Git · f399a0e5
  Christian Arnold authored 3 years ago
  
  f399a0e5
- Changed repo structure and divided templates into dev and stable, few other small changes for dev · 84562a19
  Christian Arnold authored 3 years ago
  
  84562a19
Nov 22, 2021
- Merge branch 'dt-updates' into 'master' · 0770a204
  Christian Arnold authored 3 years ago
  
  feature updates See merge request !2
  0770a204
- Merge branch 'master' into 'dt-updates' · afa73022
  Christian Arnold authored 3 years ago
  
  # Conflicts: # src/Snakemake/dev/R/consensusPeaks.R # src/Snakemake/dev/R/functions.R # src/Snakemake/dev/Snakefile
  afa73022
- various small changes before merging Rim's update for dev · 76f89bed
  Christian Arnold authored 3 years ago
  
  76f89bed
Nov 19, 2021
- added SE mode, added ChIPseq data type, other minor changes · 26b15b7a
  Rim Moussa authored 3 years ago
  
  26b15b7a
May 27, 2021
- Updated templates and other minor changes · d11203cf
  Christian Arnold authored 3 years ago
  
  d11203cf
Aug 24, 2020
- Changes to cluster.json · a1da775e
  Christian Arnold authored 4 years ago
  
  a1da775e
- General update · aa605743
  Christian Arnold authored 4 years ago
  
  aa605743
Aug 23, 2019
- Added the file runSnakemake.sh for an example call to Snakemake with Singularity · be1e27f6
  Christian Arnold authored 5 years ago
  
  be1e27f6
- Cleanup · d09c49de
  Christian Arnold authored 5 years ago
  
  d09c49de
- Cleanup · 17701599
  Christian Arnold authored 5 years ago
  
  17701599