Commits · e0553269a7255b0eb459e99afe72732bb4aecdb1 · zavolan_group / pipelines / ZARP

Feb 11, 2021
- add new docker image · e0553269
  BIOPZ-Bak Maciej authored 4 years ago
  
  e0553269
Nov 19, 2020
- ci: test new multiqc container · 7cdef5af
  BIOPZ-Bak Maciej authored 4 years ago
  
  7cdef5af
Oct 16, 2020
- - Delete unused files scripts/fg_extract_transcripts.py,... · c535a892
  BIOPZ-Gypas Foivos authored 4 years ago
  c535a892
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 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
Jun 12, 2020
- docs: rename project/workflow · a07e1173
  Alex Kanitz authored 4 years ago
  
  a07e1173
Jun 10, 2020
- refactor: use zgtf for GTF to BED12 conversion · b62f3bf1
  BIOPZ-Gypas Foivos authored 4 years ago and Alex Kanitz committed 4 years ago
  
  b62f3bf1
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 24, 2020
- Second fix in results restructuring · 27b38068
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  
  27b38068
Mar 22, 2020
- fix absolute / relative path issue in fastqc results parsing · 2792d1e6
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  
  2792d1e6
Mar 21, 2020
- use minified container images · e9d50454
  Alex Kanitz authored 5 years ago
  
  e9d50454
Mar 20, 2020
- renamed plot file 4 proper parsing · b0a1a53c
  BIOPZ-Bak Maciej authored 5 years ago
  
  b0a1a53c
- extend ALFA functionality · f5e2f6ac
  Dominik Burri authored 5 years ago and Alex Kanitz committed 5 years ago
  f5e2f6ac
Mar 19, 2020
- MultiQC · fd1e3123
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  
  fd1e3123
Mar 12, 2020
- add TIN score merge and plot steps · a0babc83
  BIOPZ-Bak Maciej authored 5 years ago
  
  a0babc83
- 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
- Merged paired end and single end rules for star_rpm and... · fb784999
  BIOPZ-Gypas Foivos authored 5 years ago
  fb784999
- 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
- 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
- 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
- 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
Feb 20, 2020
- create log directories in Snakefile\ · 5e1ec85e
  Alex Kanitz authored 5 years ago
  5e1ec85e
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
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
- fix various small issues · 17818f4a
  Alex Kanitz authored 5 years ago
  17818f4a
Jan 24, 2020
- update test input files · 4e99b664
  BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago
  4e99b664
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
- Remove prepare_annotation directory. Rename process_data to snakemake. · cb46aa34
  BIOPZ-Gypas Foivos authored 5 years ago
  
  cb46aa34
Dec 13, 2019
- Started working on subpipelines · cd2052dd
  CJHerrmann authored 5 years ago
  
  cd2052dd
Feb 19, 2019
- Addition of basic steps for process data · 52c1de75
  BIOPZ-Gypas Foivos authored 6 years ago
  
  52c1de75