Commits · cf8cf5f6b478e819cc9cf2fe36d5353c405f5da1 · Cervin Guyomar / workflows · GitLab

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Mar 15, 2019
- change resulting recalibration table files as temporary · cf8cf5f6
  mariabernard authored 6 years ago
  
  cf8cf5f6
Mar 14, 2019
- change bgzip\tabix management and temp files definition · 9d905ba1
  mariabernard authored 6 years ago
  
  9d905ba1
- bug fixed in gatk applyrecalibration trainingset syntax · 305e3911
  mariabernard authored 6 years ago
  
  305e3911
- add tabix dependancies · 3600f391
  mariabernard authored 6 years ago
  
  3600f391
- bug fixed in output files names · 7f7fcd0e
  mariabernard authored 6 years ago
  
  7f7fcd0e
- add minimum base quality threshold parameter · 8f9e6b0d
  mariabernard authored 6 years ago
  
  8f9e6b0d
Mar 05, 2019
- split_vcf need that input vcf is indexed with tabix · acb110be
  mariabernard authored 6 years ago
  
  acb110be
- fastqc has different behavior on .fq or .fastq file · 445992e0
  mariabernard authored 6 years ago
  
  445992e0
Mar 04, 2019
- comment print · 05377949
  mariabernard authored 6 years ago
  
  05377949
- add bcftools dependancy · 8e6ef271
  mariabernard authored 6 years ago
  
  8e6ef271
- rename output dir like IMAGE_calling output dire · e73a08a5
  mariabernard authored 6 years ago
  
  e73a08a5
- add basics rules md5/bgzip/tabix · 5b7b8a5e
  mariabernard authored 6 years ago
  
  5b7b8a5e
Feb 22, 2019
- add vcftools.pm in PERL5LIB, export tabix in PATH and debug concat_uniq · 419fa2f1
  Philippe Bardou authored 6 years ago
  
  419fa2f1
Feb 20, 2019
- add hardfiltering, splitvcf and vqsr rules · 7d9059dc
  Maria Bernard authored 6 years ago
  
  7d9059dc
- rename gatk_variantFiltration to IMAGE_vqsr · bcf64f55
  Maria Bernard authored 6 years ago
  
  bcf64f55
Feb 19, 2019
- update toc · d9bbe3c1
  Maria Bernard authored 6 years ago
  
  d9bbe3c1
- TOC not supported in gitlab · b00a3f32
  Maria Bernard authored 6 years ago
  
  b00a3f32
- update README · 984772ab
  Maria Bernard authored 6 years ago
  
  984772ab
- correct few mistake and input data test · d24d8ab1
  mariabernard authored 6 years ago
  
  d24d8ab1
Feb 15, 2019
- Merge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into develop · b796af1b
  mariabernard authored 6 years ago
  
  b796af1b
- update genologin usage script and test_datafile · e4a1e671
  Maria Bernard authored 6 years ago
  
  e4a1e671
- Merge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into develop · f5727de9
  mariabernard authored 6 years ago
  
  f5727de9
- update doc and test data · 9e5b7dfb
  Maria Bernard authored 6 years ago
  
  9e5b7dfb
- remove useless file · 1d2c50a0
  Maria Bernard authored 6 years ago
  
  1d2c50a0
- update test data · d56759e8
  Maria Bernard authored 6 years ago
  
  d56759e8
Feb 13, 2019
- rename workflow IMAGE in IMAGE_calling · 4f0e3584
  Maria Bernard authored 6 years ago
  
  4f0e3584
- rename workflow IMAGE in IMAGE_calling · 7760ab37
  Maria Bernard authored 6 years ago
  
  7760ab37
- add qualimap in resources_SLURM.yaml and update mem for recalibration · e89b5e8a
  Maria Bernard authored 6 years ago
  
  e89b5e8a
Dec 31, 2018
- simplifies some rules, remove parallelisation by chromosom, add combine and genotype GVCF from GATK · 7361b488
  mariabernard authored 6 years ago
  
  7361b488
- simplifies some rules, remove parallelisation by chromosom, add combine and genotype GVCF from GATK · e14d2347
  mariabernard authored 6 years ago
  
  e14d2347
Oct 29, 2018
- variant calling multiple for IMAGE project · 8aa366ab
  Kenza Bazi-Kabbaj authored 6 years ago
  
  8aa366ab
- add test data and first rule intersect_vcf.smk · 08b3ffaf
  mariabernard authored 6 years ago and Kenza Bazi-Kabbaj committed 6 years ago
  
  08b3ffaf
- gat_variantFiltration, initialisation workflow · de9f4253
  mariabernard authored 6 years ago and Kenza Bazi-Kabbaj committed 6 years ago
  
  de9f4253
- fix bug sample merging · 52badb4b
  Kenza Bazi-Kabbaj authored 6 years ago
  
  52badb4b
- fix bug phred quality · 03f15728
  Kenza Bazi-Kabbaj authored 6 years ago
  
  03f15728
- 1000GB · d0b24f33
  Kenza Bazi-Kabbaj authored 6 years ago
  
  d0b24f33
- delete old version · 54f065cf
  Kenza Bazi-Kabbaj authored 6 years ago
  
  54f065cf
- snakemake template : (re)correct star_index variable and on Results output dir · 2ae8e0c5
  mariabernard authored 6 years ago and Kenza Bazi-Kabbaj committed 6 years ago
  
  2ae8e0c5
- Snakemkae template : go back · 4f311331
  mariabernard authored 6 years ago and Kenza Bazi-Kabbaj committed 6 years ago
  
  4f311331
- Snakemake template : bug in star rule dependancies · 7ffcf831
  Maria Bernard authored 6 years ago and Kenza Bazi-Kabbaj committed 6 years ago
  
  7ffcf831