Commits · 78490710d12f00675086352fb1230f8e37ad02c2 · Cervin Guyomar / workflows · GitLab

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Mar 31, 2020
- Snakemake 1000RNASeq ASE : debug vcf_annotator, change script in execution... · 78490710
  mariabernard authored 4 years ago
  
  Snakemake 1000RNASeq ASE : debug vcf_annotator, change script in execution mode, correct VCF_for_ASE_and_table rule
  78490710
- Snakemake 1000RNASeq ASE : add summary script for trimgalore, star and to convert phred scale · bbefebc2
  mariabernard authored 4 years ago
  
  bbefebc2
- Snakemake 1000RNASeq ASE : add script dir in PATH · fed78720
  mariabernard authored 4 years ago
  
  fed78720
- Snakemake 1000RNASeq ASE : add bedtools dependency in config.yaml · cc119ef2
  mariabernard authored 4 years ago
  
  cc119ef2
Mar 25, 2020
- Merge branch 'develop' of forgemia.inra.fr:bios3biol/workflows into develop · 7b501310
  mariabernard authored 4 years ago
  
  7b501310
- Snakemake 1000RNASeq ASE: correct GATK4 VariantFiltration filter syntaxe · b79e1146
  mariabernard authored 4 years ago
  
  b79e1146
- Snakemake 1000RNASeq ASE: add quality trimming threshold in Trimgalore rules · 77964609
  mariabernard authored 4 years ago
  
  77964609
- Snakemake 1000RNASeq ASE: correct script syntax in gtf2bed rule · 81f12447
  mariabernard authored 4 years ago
  
  81f12447
- Snakemake RNAseqVariantCalling : report 1000RRNASeq_chicken/calling update:... · b371fa5e
  Maria Bernard authored 4 years ago
  
  Snakemake RNAseqVariantCalling : report 1000RRNASeq_chicken/calling update: quality trimming and trimgalore_summary
  b371fa5e
- Merge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into develop · 7d39cde8
  Maria Bernard authored 4 years ago
  
  7d39cde8
- Snakemake 1000RNASeq : add fastq quality filtering threshol at 15 by default · 99b7067f
  Maria Bernard authored 4 years ago
  
  99b7067f
- 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