Commits · 9990cea6b7583777f9e2580acd80b9a8f181772e · Cervin Guyomar / workflows · GitLab

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

Jun 19, 2019
- 1000RNASEQ chicken ASE: add fasta dict and bam indexes in SplitNCigar rule · 9990cea6
  mariabernard authored 5 years ago
  
  9990cea6
- 1000RNASEQ chicken ASE: correct index Fasta mem in Snakefile · 1793da7e
  mariabernard authored 5 years ago
  
  1793da7e
- 1000RNASEQ chicken ASE: correct wildcard constraint, rmdup command line and... · 21fe7968
  mariabernard authored 5 years ago
  
  1000RNASEQ chicken ASE: correct wildcard constraint, rmdup command line and add fasta index as input in SplitCigar
  21fe7968
- 1000RNASEQ chicken ASE: add bai inputs, correct phaser.py commande line · c06b562c
  mariabernard authored 5 years ago
  
  c06b562c
- 1000RNASEQ chicken ASE: add fasta indexing rules · 1ce61910
  mariabernard authored 5 years ago
  
  1ce61910
- 1000RNASEQ chicken ASE: update dependencies in config.yaml · 5ec6c951
  mariabernard authored 5 years ago
  
  5ec6c951
Jun 11, 2019
- 1000RNASEQ_chicken/ASE : correction of phASER command line · d3750705
  mariabernard authored 5 years ago
  
  d3750705
Jun 07, 2019
- 1000RNASeq_chicken ASE : debug STAR_Index_1 rule · 3e61306d
  mariabernard authored 5 years ago
  
  3e61306d
- 1000RNASeq_chicken ASE : change rule names · a368aae1
  mariabernard authored 5 years ago
  
  a368aae1
- 1000RNASeq_chicken ASE : change tools dependencies in config.yaml · 82bf6f0c
  mariabernard authored 5 years ago
  
  82bf6f0c
- 1000RNASeq_chicken ASE : add md5sum doc in config.yaml · 28a3a595
  mariabernard authored 5 years ago
  
  28a3a595
- 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