Commits · master · Cervin Guyomar / workflows · GitLab

15 Jan, 2021 1 commit
- Snakemake : (re) add rules · 055a8c60
  mariabernard authored Jan 15, 2021
  
  055a8c60
08 Dec, 2020 8 commits
- Merge branch 'develop' · 03b2e61c
  Maria Bernard authored Dec 08, 2020
  
  03b2e61c
- change author affiliation · 72d966e3
  Maria Bernard authored Dec 08, 2020
  
  72d966e3
- merge develop · f7e2c87b
  Maria Bernard authored Dec 08, 2020
  
  f7e2c87b
- update README · 4551ebe5
  Maria Bernard authored Dec 08, 2020
  
  4551ebe5
- update README · 7ef3cf9d
  Maria Bernard authored Dec 08, 2020
  
  7ef3cf9d
- add image · e7677d9a
  mariabernard authored Dec 08, 2020
  
  e7677d9a
- change string encoding in variantFiltration · 00b17e5c
  mariabernard authored Dec 08, 2020
  
  00b17e5c
- add phaser_expr_matrix · 547ed035
  mariabernard authored Dec 08, 2020
  
  547ed035
29 Jul, 2020 1 commit
- Snakemake 1000RNASeq_chicken/calling : update STAR Aln memory resource · 32023f08
  mariabernard authored Jul 29, 2020
  
  32023f08
12 Jun, 2020 2 commits
- Merge branch 'develop' · 5e59c856
  mariabernard authored Jun 12, 2020
  
  5e59c856
- Snakemake RNAseqVariantCalling: finalization of RNAseqVariantCalling pipeline · 33ef13bc
  mariabernard authored Jun 12, 2020
  
  33ef13bc
08 Jun, 2020 1 commit
- 1000RNASeq calling: change partition attribut name in resources_SLURM.yaml · 30b71c61
  mariabernard authored Jun 08, 2020
  
  30b71c61
05 Jun, 2020 3 commits
- RNASeqVariantCalling : rename Snakefile · 093af7f4
  mariabernard authored Jun 05, 2020
  
  093af7f4
- Snakemake RNSAseqVariantCalling : update documentation workflow and clean up · b47fcd24
  Maria Bernard authored Jun 05, 2020
  
  b47fcd24
- 1000RNASeq_chicken/ASE : finalize snakemake pipeline · d88486bc
  mariabernard authored Jun 05, 2020
  
  d88486bc
22 Apr, 2020 4 commits
- Resolve conflict before merging · 9ae7f1ff
  mariabernard authored Apr 22, 2020
  
  9ae7f1ff
- Snakemake 1000RNASeq chicken/ase : add developpment status in the README file · 9fd709fb
  mariabernard authored Apr 22, 2020
  
  9fd709fb
- Snakemake 1000RNASeq chicken/ase : change variant filtering procedure and update ressources · 020ab5ff
  mariabernard authored Apr 22, 2020
  
  020ab5ff
- Snakemake 1000RNASeq chicken/calling : update SLURM.sh · eb035918
  mariabernard authored Apr 22, 2020
  
  eb035918
31 Mar, 2020 4 commits
- Snakemake 1000RNASeq ASE : debug vcf_annotator, change script in execution... · 78490710
  mariabernard authored Mar 31, 2020
```
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 Mar 31, 2020
  
  bbefebc2
- Snakemake 1000RNASeq ASE : add script dir in PATH · fed78720
  mariabernard authored Mar 31, 2020
  
  fed78720
- Snakemake 1000RNASeq ASE : add bedtools dependency in config.yaml · cc119ef2
  mariabernard authored Mar 31, 2020
  
  cc119ef2
25 Mar, 2020 9 commits
- Merge branch 'develop' of forgemia.inra.fr:bios3biol/workflows into develop · 7b501310
  mariabernard authored Mar 25, 2020
  
  7b501310
- Snakemake 1000RNASeq ASE: correct GATK4 VariantFiltration filter syntaxe · b79e1146
  mariabernard authored Mar 25, 2020
  
  b79e1146
- Snakemake 1000RNASeq ASE: add quality trimming threshold in Trimgalore rules · 77964609
  mariabernard authored Mar 25, 2020
  
  77964609
- Snakemake 1000RNASeq ASE: correct script syntax in gtf2bed rule · 81f12447
  mariabernard authored Mar 25, 2020
  
  81f12447
- Snakemake RNAseqVariantCalling : report 1000RRNASeq_chicken/calling update:... · b371fa5e
  Maria Bernard authored Mar 25, 2020
```
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 Mar 25, 2020
  
  7d39cde8
- Snakemake 1000RNASeq : add fastq quality filtering threshol at 15 by default · 99b7067f
  Maria Bernard authored Mar 25, 2020
  
  99b7067f
- 1000RNASeq calling : bug fix in script/trimgalore_summary.py when sample are... · b2a0cf0b
  mariabernard authored Mar 25, 2020
```
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 Mar 25, 2020
  
  17359c00
23 Mar, 2020 4 commits
- Snakemake 1000RNASeq ASE: change Results output directory name in Results_ASE · e493d0c6
  mariabernard authored Mar 23, 2020
  
  e493d0c6
- Snakemake 1000RNASeq ASE: update config comment · 587e68eb
  mariabernard authored Mar 23, 2020
  
  587e68eb
- Snakemake 1000RNASeq ASE : update dependency version · 7803ae62
  Maria Bernard authored Mar 23, 2020
  
  7803ae62
- Snakemake 1000RNASeq ASE: remove useless genomemasking rule · 398d76f5
  Maria Bernard authored Mar 23, 2020
  
  398d76f5
13 Mar, 2020 3 commits
- 1000RNASeq ASE : add gtf2bed script · 1f3261fb
  Maria Bernard authored Mar 13, 2020
  
  1f3261fb
- 1000RNASeq ASE : add some changes from initial version uncommit · 7347a093
  Maria Bernard authored Mar 13, 2020
  
  7347a093
- 1000RNASeq chicken : add new ASE pipeline · 9d4969ae
  Maria Bernard authored Mar 13, 2020
  
  9d4969ae