Commits · c5f7bfdae6b01c9412a01fe1104f8b83c839383f · Christian Arnold / ATACSeq_Snakemake · GitLab

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Mar 23, 2023
- misc · c5f7bfda
  Christian Arnold authored 1 year ago
  
  c5f7bfda
Mar 21, 2023
- change multiqc config file back to an absolute path · a1d50bd8
  Christian Arnold authored 1 year ago
  
  a1d50bd8
- misc · e3a40ec4
  Christian Arnold authored 1 year ago
  
  e3a40ec4
- make PCA script more failure proof · 0014dcc7
  Christian Arnold authored 1 year ago
  
  0014dcc7
- Create dirs if they dont exist yet · d9d165fd
  Christian Arnold authored 1 year ago
  
  d9d165fd
- Small bugfixes related to ChIP-Seq input control and small number of peaks that crash ChIPSeeker · bbf39324
  Christian Arnold authored 1 year ago
  
  bbf39324
Oct 11, 2022
- Added /g/zaugg to params.sh templates · 65f7fb56
  Christian Arnold authored 2 years ago
  
  65f7fb56
Sep 14, 2022
- Updated Snakemake wrapper · fe1ff607
  Christian Arnold authored 2 years ago
  
  fe1ff607
Jun 14, 2022
- Small fixes · 6fa4b771
  Christian Arnold authored 2 years ago
  
  6fa4b771
Jun 10, 2022
- Update functions.R · 594924be
  Christian Arnold authored 2 years ago
  
  594924be
Jun 02, 2022
- Fix for 0 consensus peaks resulting from DiffBind column rename · e37f923d
  Christian Arnold authored 2 years ago
  
  e37f923d
- Added missing rules to cluster.config for enhanced customization · cddd2087
  Christian Arnold authored 2 years ago
  
  cddd2087
May 30, 2022
- Removed the replicate_No column as requirement from the sample file · e7e22fba
  Christian Arnold authored 2 years ago
  
  e7e22fba
May 17, 2022
- Fixed bug with new DiffBind that causes 0 consensus peaks · 61619e98
  Christian Arnold authored 2 years ago
  
  61619e98
- 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