Commits · b2a0cf0bfca5b249c0a41a3d096c51ee2fa5198a · Cervin Guyomar / workflows · GitLab

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Opération de maintenance au data center INRAE de Toulouse du jeudi 20 mars à 15h00 au lundi 24 Mars 2025 à 13h
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Mar 25, 2020
- 1000RNASeq calling : bug fix in script/trimgalore_summary.py when sample are... · b2a0cf0b
  mariabernard authored 4 years ago
  
  1000RNASeq calling : bug fix in script/trimgalore_summary.py when sample are all single end sequenced
  b2a0cf0b
- SNakemake 1000RNASeq ASE: comment phaser_expr_matrix part · 17359c00
  Maria Bernard authored 4 years ago
  
  17359c00
Mar 23, 2020
- Snakemake 1000RNASeq ASE: change Results output directory name in Results_ASE · e493d0c6
  mariabernard authored 4 years ago
  
  e493d0c6
- Snakemake 1000RNASeq ASE: update config comment · 587e68eb
  mariabernard authored 4 years ago
  
  587e68eb
- Snakemake 1000RNASeq ASE : update dependency version · 7803ae62
  Maria Bernard authored 4 years ago
  
  7803ae62
- Snakemake 1000RNASeq ASE: remove useless genomemasking rule · 398d76f5
  Maria Bernard authored 4 years ago
  
  398d76f5
Mar 13, 2020
- 1000RNASeq ASE : add gtf2bed script · 1f3261fb
  Maria Bernard authored 5 years ago
  
  1f3261fb
- 1000RNASeq ASE : add some changes from initial version uncommit · 7347a093
  Maria Bernard authored 5 years ago
  
  7347a093
- 1000RNASeq chicken : add new ASE pipeline · 9d4969ae
  Maria Bernard authored 5 years ago
  
  9d4969ae
- 1000RNASeq chicken : remove ASE pipeline · a4c5a1e5
  Maria Bernard authored 5 years ago
  
  a4c5a1e5
Nov 25, 2019
- Update README.md · 9afdc55d
  Celine Noirot authored 5 years ago
  
  9afdc55d
Oct 04, 2019
- 1000RNASeq ASE : add call_rate_filter output, per genotype and coverage per group in TSV format · e48126ae
  mariabernard authored 5 years ago
  
  e48126ae
- 1000RNASeq ASE : correct concatenation of string and int in exclude_non_var.py · 84943fe2
  mariabernard authored 5 years ago
  
  84943fe2
Sep 11, 2019
- 1000RNASeq ASE : uncomment input/output parameter in call_rate_filter.py · b88cfb86
  mariabernard authored 5 years ago
  
  b88cfb86
- Merge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into develop · c3eb22dd
  mariabernard authored 5 years ago
  
  c3eb22dd
- 1000RNASeq ASE : add function to call_rate_filter.py, to split genotype and... · 0ce4c21a
  mariabernard authored 5 years ago
  
  1000RNASeq ASE : add function to call_rate_filter.py, to split genotype and allelel depth by group in TSV files
  0ce4c21a
Aug 28, 2019
- 1000RNASEq Calling : complete authhor · a6b23f01
  Maria Bernard authored 5 years ago
  
  a6b23f01
- 1000RNASEq Calling : add TOC in README · 38c1162c
  Maria Bernard authored 5 years ago
  
  38c1162c
- 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