Commits · c3e523c88837fe2c5ac55bda315bfb42812ba607 · Cervin Guyomar / workflows · GitLab

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May 15, 2019
- 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
- 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 6 years ago
  
  84aba97a
- IMAGE_vqsr, change config.yaml how to generat sample_mean_cov.tsv · 7f5d7de3
  mariabernard authored 6 years ago
  
  7f5d7de3
Apr 12, 2019
- add Snakemake SNP calling on RNASeq · 70a4e071
  Maria Bernard authored 6 years ago
  
  70a4e071
Apr 11, 2019
- IMAGE_calling : perfomr combineGVCF by cohort · 4f81b131
  Maria Bernard authored 6 years ago
  
  4f81b131
- IMAGE_calling : propose resources with memGlobal per job · 0f973de8
  mariabernard authored 6 years ago
  
  0f973de8
- IMAGE_calling : remove protected statement and improve cpu resources · 9136fb7d
  mariabernard authored 6 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
Mar 28, 2019
- uncomment md5 output files · 756ae24e
  Maria Bernard authored 6 years ago
  
  756ae24e
- add test data · 80229158
  Maria Bernard authored 6 years ago
  
  80229158
- remove rule bgzip, and compressed vcf in previous rule, add on success code to... · a8c0bf77
  Maria Bernard authored 6 years ago
  
  remove rule bgzip, and compressed vcf in previous rule, add on success code to remove additionnal temps files
  a8c0bf77
- IMAGE_calling : remove Bio import · bcf69dc9
  Maria Bernard authored 6 years ago
  
  bcf69dc9
- add cluster partition resources in IMAGE workflows · f019a282
  Maria Bernard authored 6 years ago
  
  f019a282
- IMAGE workflows : add few changes about temp files and output files · af575796
  Maria Bernard authored 6 years ago
  
  af575796
- add genotype filtering step · 49a6acef
  Maria Bernard authored 6 years ago
  
  49a6acef
- add workflow image · 2fa878be
  Maria Bernard authored 6 years ago
  
  2fa878be
- change hardfiltering parameter · b760a0e4
  Maria Bernard authored 6 years ago
  
  b760a0e4
- add README file · 1439a3dc
  Maria Bernard authored 6 years ago
  
  1439a3dc
Mar 15, 2019
- change fastqc resources · 5700a073
  mariabernard authored 6 years ago
  
  5700a073
- 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