Commits · 09ca6d67301d28e879061d7aaf17aba93fcbeed8 · Cervin Guyomar / workflows · GitLab

Snippets Groups Projects

Aug 28, 2019
- 1000RNASEq Calling : add a full documentation · 09ca6d67
  Maria Bernard authored 5 years ago
  
  09ca6d67
- Merge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into develop · 6437bb31
  Maria Bernard authored 5 years ago
  
  6437bb31
- 1000RNASEq Calling : move population.tsv.example to data · c078ee55
  Maria Bernard authored 5 years ago
  
  c078ee55
- 1000RNASEq Calling : add test data · ee2bcc86
  Maria Bernard authored 5 years ago
  
  ee2bcc86
Aug 27, 2019
- 1000RNASeq : add phASER id_separator option · cf26c1ba
  mariabernard authored 5 years ago
  
  cf26c1ba
- 1000RNASeq : correct header of call_rate_filter.py · b1ba7ce5
  mariabernard authored 5 years ago
  
  b1ba7ce5
Aug 26, 2019
- 1000RNASeq : add vcf index file as rule input · 6518e3a2
  mariabernard authored 5 years ago
  
  6518e3a2
- 1000RNASeq : correct log input files and log text · c5b055fb
  mariabernard authored 5 years ago
  
  c5b055fb
- 1000RNASeq : add log summary output files in Snakefile · b913a259
  mariabernard authored 5 years ago
  
  b913a259
- 1000RNASeq : add vcfFilterSummary rule · d4f07ac3
  mariabernard authored 5 years ago
  
  d4f07ac3
- 1000RNASeq : add temp statement and correct SJ_out filter rule in alignmentProcess rules · 94e804ce
  mariabernard authored 5 years ago
  
  94e804ce
- 1000RNASeq : correct path to script dir in TrimGalore rules · 036bce5a
  mariabernard authored 5 years ago
  
  036bce5a
Aug 23, 2019
- 1000RNASeq ASE: add summary statistics for vcf filtering and add vcf index as... · 20d62040
  mariabernard authored 5 years ago
  
  1000RNASeq ASE: add summary statistics for vcf filtering and add vcf index as input in variantFiltration
  20d62040
- 1000RNASeq ASE: add summary statistics for trimming mappin and vcf filtering · 94718a12
  mariabernard authored 5 years ago
  
  94718a12
- 1000RNASeq ASE: add is_gzip function and change ValidGRoup by Valid_CR_group · 5539d7d9
  mariabernard authored 5 years ago
  
  5539d7d9
- Merge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into develop · 149a034f
  mariabernard authored 5 years ago
  
  149a034f
- 1000RNASeq ASE: add filtered VCF file in final ouput list · afc3e0e2
  mariabernard authored 5 years ago
  
  afc3e0e2
Aug 22, 2019
- 1000RNASeq ASE: remove ">" in VCF header in exclude_non_var.py · 5904d383
  Maria Bernard authored 5 years ago
  
  5904d383
- 1000RNASeq ASE: debug writing VCF header line in exclude_non_var.py · eeebf08b
  Maria Bernard authored 5 years ago
  
  eeebf08b
Aug 21, 2019
- 1000RNASeq ASE: read files in text mode not binary, and improve exclude_non_var.py log · 0f66f769
  mariabernard authored 5 years ago
  
  0f66f769
- 1000RNASeq ASE: change variant filtration results directories and remove var... · c8bd62c1
  mariabernard authored 5 years ago
  
  1000RNASeq ASE: change variant filtration results directories and remove var wildcards (only work on SNP)
  c8bd62c1
- 1000RNASeq ASE: change variant filtration results directories and remove var... · 41a3bd4d
  mariabernard authored 5 years ago
  
  1000RNASeq ASE: change variant filtration results directories and remove var wildcards (only work on SNP)
  41a3bd4d
- 1000RNASeq ASE: add wildcard constraints in bgzip rule · 041ae378
  mariabernard authored 5 years ago
  
  041ae378
- 1000RNASeq ASE: add ability to read gziped file in script · 74ea1f9f
  Maria Bernard authored 5 years ago
  
  74ea1f9f
- 1000RNASeq ASE: correct script directory path in VarForMasking and callRateFilter rules · 4d4b4979
  Maria Bernard authored 5 years ago
  
  4d4b4979
- 1000RNASeq ASE: change default value for call_rate_threshold in config.yaml.example · c7efe3ec
  Maria Bernard authored 5 years ago
  
  c7efe3ec
- 1000RNASeq ASE: add message in VarForMasking and callRateFilter rules · 5407285e
  Maria Bernard authored 5 years ago
  
  5407285e
- 1000RNASeq ASE: correct data/population.tsv.example · 28d0bc5b
  Maria Bernard authored 5 years ago
  
  28d0bc5b
- 1000RNASeq ASE: debug script/call_rate_filter.py and add... · 67ad2a5c
  Maria Bernard authored 5 years ago
  
  1000RNASeq ASE: debug script/call_rate_filter.py and add script/exclude_non_var.py instead of SelectVariant in VariantFiltration.smk
  67ad2a5c
- 1000RNASeq ASE: add doc in config.yaml · 93f79fab
  Maria Bernard authored 5 years ago
  
  93f79fab
Aug 19, 2019
- 1000RNASeq/ASE : take all SJ_out file as input for STAR 2 indexing · 2802e78f
  Maria Bernard authored 5 years ago
  
  2802e78f
- 1000RNASeq/ASE : small doc and resources update · 5983b0bb
  Maria Bernard authored 5 years ago
  
  5983b0bb
- 1000RNASeq ASE : add call rate filtering · 686961f0
  Maria Bernard authored 5 years ago
  
  686961f0
Aug 14, 2019
- 1000RNASeq/ASE : change STAR 2 pass strategies · ff6cc295
  Maria Bernard authored 5 years ago
  
  ff6cc295
Jul 02, 2019
- Update README.md · 496b7186
  Celine Noirot authored 5 years ago
  
  496b7186
- debug jar package calling · 712bd373
  Celine Noirot authored 5 years ago
  
  712bd373
- Update README.md · 73d72b91
  Celine Noirot authored 5 years ago
  
  73d72b91
- doc update · 48d355e9
  Celine Noirot authored 5 years ago
  
  48d355e9
- Update doc · cb61ac35
  Celine Noirot authored 5 years ago
  
  cb61ac35
Jul 01, 2019
- documentation · 10132ef2
  Celine Noirot authored 5 years ago
  
  10132ef2