Commits · c79bb96e6330bb30d931cc81b6ed644657bc2c3b · zavolan_group / pipelines / ZARP · GitLab

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Mar 12, 2020
- include test_alfa in CI · c79bb96e
  Dominik Burri authored 5 years ago
  
  c79bb96e
- added alfa_indexes to config.yaml · a7dddfe6
  Dominik Burri authored 5 years ago
  
  a7dddfe6
- 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 07, 2020
- Merge branch 'combine_star_rpm_rule' into 'master' · 9f2e0a67
  Alex Kanitz authored 5 years ago
  9f2e0a67
Mar 06, 2020
- Merged paired end and single end rules for star_rpm and... · fb784999
  BIOPZ-Gypas Foivos authored 5 years ago
  fb784999
- Merge branch 'replace_cufflinks_image_with_gffread_image' into 'master' · 5f98edf3
  BIOPZ-Gypas Foivos authored 5 years ago
  5f98edf3
- Replace cufflinks image with gffread image · c3d15275
  BIOPZ-Gypas Foivos authored 5 years ago
  
  c3d15275
- Generate bedgraph file of normalised coverage. Fixes #45 · 2dfb1c2c
  BIOPZ-Gypas Foivos authored 5 years ago
  
  2dfb1c2c
- 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 · 7784fc9b
  BIOPZ-Gypas Foivos authored 5 years ago
  
  7784fc9b
- 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
- Closes #76 and #79 · 88e3914b
  BIOPZ-Gypas Foivos authored 5 years ago
  
  88e3914b
- 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
- Merge branch 'generate_gene_count_tables_from_salmon' into 'master' · f31261b5
  Alex Kanitz authored 5 years ago
  f31261b5
- 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
- Merge branch 'use_minified_docker_images' into 'master' · 0c039203
  Alex Kanitz authored 5 years ago
  0c039203
- Use minified docker images · dc2afcf9
  Alex Kanitz authored 5 years ago
  
  dc2afcf9
- Merge branch 'generate_gene_count_tables' into 'master' · 13975de8
  Alex Kanitz authored 5 years ago
  13975de8
- 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
- Merge branch 'input_features' into 'master' · 641f2cbb
  Alex Kanitz authored 5 years ago
  641f2cbb
- 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
- Merge branch 'log_dirs' into 'master' · c58f28df
  Alex Kanitz authored 5 years ago
  c58f28df
- create log directories in Snakefile\ · 5e1ec85e
  Alex Kanitz authored 5 years ago
  5e1ec85e
Feb 18, 2020
- Merge branch 'hotfix_docs_missing_link' into 'master' · 1f933bcc
  Alex Kanitz authored 5 years ago
  1f933bcc
- fix broken links in docs · 1782ea86
  Alex Kanitz authored 5 years ago
  
  1782ea86
- Merge branch 'conda_env' into 'master' · 885c5692
  Alex Kanitz authored 5 years ago
  885c5692
- install dependencies via Conda · 8742cd72
  Alex Kanitz authored 5 years ago
  8742cd72
- Merge branch 'verbose_tests' into 'master' · 4ad34d82
  Alex Kanitz authored 5 years ago
  4ad34d82
- run tests in verbose mode · 0d95577e
  Alex Kanitz authored 5 years ago
  0d95577e
Feb 17, 2020
- Merge branch 'TIN' into 'master' · ba39b976
  Alex Kanitz authored 5 years ago
  ba39b976
- add TIN score calculation · c538fe8b
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  c538fe8b
Feb 15, 2020
- Merge branch 'labkey_api_input_parser' into 'master' · a654943c
  Alex Kanitz authored 5 years ago
  a654943c
- 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
- Merge branch 'recommended_repo_structure' into 'master' · fdc358f4
  Alex Kanitz authored 5 years ago
  fdc358f4
- repo follows recommended structure · 1e52fa56
  Alex Kanitz authored 5 years ago
  
  1e52fa56
- Merge branch 'hotfix_integration_test' into 'master' · 39b7ea7b
  Alex Kanitz authored 5 years ago
  39b7ea7b
- hot fix integration test script · 3fe8f0d1
  Alex Kanitz authored 5 years ago
  
  3fe8f0d1
- Merge branch 'merge_api_input_parse' into 'master' · e7ac9662
  Alex Kanitz authored 5 years ago
  e7ac9662