Commits · 8793fa4ac786a2542eb49ff02c5e86b99a3fd8e3 · Cervin Guyomar / workflows · GitLab

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A compter du 1er avril, attention à vos pipelines : Nouvelles limitations de Docker Hub

Jun 07, 2019
- 1000RNASeq_chicken ASE : perform rmdup for single end read · 8793fa4a
  mariabernard authored 5 years ago
  
  8793fa4a
- 1000RNASeq_chicken ASE : do not use bin variable in config file for basic rule · 274dafc9
  mariabernard authored 5 years ago
  
  274dafc9
Jun 06, 2019
- 1000RNASEQ_chicken/ASE : rename Snakefile in SLURM.sh · 3730d27f
  mariabernard authored 5 years ago
  
  3730d27f
- 1000RNASEQ_chicken/ASE : rename Snakefile · a2aac4e7
  mariabernard authored 5 years ago
  
  a2aac4e7
- 1000RNASEQ_chicken/ASE : change GATK version · 5e2e5426
  mariabernard authored 5 years ago
  
  5e2e5426
May 16, 2019
- Merge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into develop · 0fd7d540
  Maria Bernard authored 5 years ago
  
  0fd7d540
- 1000RNASeq_chicken ASE : add ASE snakemake workflow · 1859581e
  Maria Bernard authored 5 years ago
  
  1859581e
- IMAGE_calling : bug in config.yaml to run the test · dbc629ef
  mariabernard authored 5 years ago
  
  dbc629ef
May 15, 2019
- IMAGE_calling : add snakemake command line that use global memory instead of memory per cpu · 6c32d145
  Philippe Bardou authored 5 years ago
  
  6c32d145
- IMAGE_calling bug in type of option nb_in_cohort · 4ae146ce
  Philippe Bardou authored 5 years ago
  
  4ae146ce
- IMAGE_calling :remove not allowed multithreading in GATK command line · e83e6d1a
  Philippe Bardou authored 5 years ago
  
  e83e6d1a
- IMAGE_vqsr : removing debugging print · 6ad5173a
  mariabernard authored 5 years ago
  
  6ad5173a
- Merge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into develop · 9aaf76d2
  mariabernard authored 5 years ago
  
  9aaf76d2
- IMAGE_vqsr : Execute VQSR on split SNP/INDEL GATK variant, not on full GATK variants · e5d63417
  mariabernard authored 5 years ago
  
  e5d63417
- IMAGE_vqse : replace vcf-isec by bcftools isec · c3e523c8
  mariabernard authored 5 years ago
  
  c3e523c8
- IMAGE_vqsr : add script dir in PATH to execute filter_multi_samples_vcf.py · 63746344
  mariabernard authored 5 years ago
  
  63746344
- IMAGE_vqsr : update resources · 8e5deb30
  mariabernard authored 5 years ago
  
  8e5deb30
May 02, 2019
- 1000RNASeq_chicken_calling : pandas read_table deprecated, use read_csv with sep='\t' · 69ced2dc
  mariabernard authored 5 years ago
  
  69ced2dc
- IMAGE_calling : add temp dir for samtools sort · a738bcfe
  mariabernard authored 5 years ago
  
  a738bcfe
Apr 25, 2019
- IMAGE_vqsr, use gatk_prefix instead of variants_gatk in bcftools_stat rule · 84aba97a
  mariabernard authored 5 years ago
  
  84aba97a
- IMAGE_vqsr, change config.yaml how to generat sample_mean_cov.tsv · 7f5d7de3
  mariabernard authored 5 years ago
  
  7f5d7de3
Apr 12, 2019
- add Snakemake SNP calling on RNASeq · 70a4e071
  Maria Bernard authored 5 years ago
  
  70a4e071
Apr 11, 2019
- IMAGE_calling : perfomr combineGVCF by cohort · 4f81b131
  Maria Bernard authored 5 years ago
  
  4f81b131
- IMAGE_calling : propose resources with memGlobal per job · 0f973de8
  mariabernard authored 5 years ago
  
  0f973de8
- IMAGE_calling : remove protected statement and improve cpu resources · 9136fb7d
  mariabernard authored 5 years ago
  
  9136fb7d
Apr 04, 2019
- IMAGE_vqsr : rename recal.idx output files · ce97ae6e
  mariabernard authored 6 years ago
  
  ce97ae6e
- IMAGE_vqsr : add bcftools stat output in final output list and define final temp file to remove · c46684c3
  mariabernard authored 6 years ago
  
  c46684c3
- IMAGE_vqsr : bug fix in bcftools stat log file · 655feaf3
  mariabernard authored 6 years ago
  
  655feaf3
- IMAGE_vqsr: remove temp statement for tbi · 5ae0ec10
  mariabernard authored 6 years ago
  
  5ae0ec10
Apr 02, 2019
- IMAGE_vqsr : rename output and modify comment · 34ec5210
  mariabernard authored 6 years ago
  
  34ec5210
- IMAGE_vqsr : rename output and modify comment · 3a7d8927
  mariabernard authored 6 years ago
  
  3a7d8927
- IMAGE_vqsr : bcftools stat · c91e9032
  mariabernard authored 6 years ago
  
  c91e9032
Apr 01, 2019
- IMAGE vqsr: remove temp() statement for md5 rule and add it to tabix rule · ea792b8d
  mariabernard authored 6 years ago
  
  ea792b8d
- IMAGE vqsr: add bcftools stat and add logs directories · 07679bc2
  mariabernard authored 6 years ago
  
  07679bc2
- IMAGE_vqsr: add input test data · cf1fea3e
  mariabernard authored 6 years ago
  
  cf1fea3e
- IMAGE_vqsr: add --excludeFiltered option to select variant to really exclude... · 677f139a
  mariabernard authored 6 years ago
  
  IMAGE_vqsr: add --excludeFiltered option to select variant to really exclude SNP or INDEL not only tagged them
  677f139a
- IMAGE_vqsr: rename intersect rules · 8e71a481
  mariabernard authored 6 years ago
  
  8e71a481
- IMAGE_vqsr: add detailed resources requirement · 94b50f7c
  mariabernard authored 6 years ago
  
  94b50f7c
- IMAGE_vqsr: add on_success rule · af6d2d63
  mariabernard authored 6 years ago
  
  af6d2d63
- improve filter_multi_sample to take into account GATK specificity · ec072ab9
  mariabernard authored 6 years ago
  
  ec072ab9