Commits · a54ff3e8f67ca30cfe1e055360828a0f02446848 · zavolan_group / pipelines / ZARP · GitLab

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Mar 06, 2020
- 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
- hot fix integration test script · 3fe8f0d1
  Alex Kanitz authored 5 years ago
  
  3fe8f0d1
- LabKey-like input to Snakmake input · 979e6cdd
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  979e6cdd
- display rule graph instead of DAG · ff08b9c3
  CJHerrmann authored 5 years ago and Alex Kanitz committed 5 years ago
  ff08b9c3
- verify test workflow output against ground truth · c6341db2
  Alex Kanitz authored 5 years ago
  c6341db2
Feb 09, 2020
- replace test files with small synthetic ones · 48e012a0
  Alex Kanitz authored 5 years ago
  48e012a0
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
- Create two dictionary files for converting LabKey table to Snakemake inputs · 8b8e2774
  BIOPZ-Börsch Anastasiya authored 5 years ago and Alex Kanitz committed 5 years ago
  
  8b8e2774
- fix various small issues · 17818f4a
  Alex Kanitz authored 5 years ago
  17818f4a
Feb 04, 2020
- add documentation · 1ef8b6af
  Alex Kanitz authored 5 years ago
  1ef8b6af
- clean up tests · 6a231363
  Alex Kanitz authored 5 years ago
  6a231363
Feb 03, 2020
- generate Snakemake inputs from LabKey data table · cd541afe
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  cd541afe
Jan 24, 2020
- update test input files · 4e99b664
  BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago
  4e99b664
Jan 10, 2020
- added fastq test files · f492977d
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  
  f492977d
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