Commits · 71eb31625ea9803f4d7c2223e2f4dd8be9cc11bf · Xavier Grand / ChIPster

Mar 12, 2021
- bwa: fix file_id definition · 71eb3162
  Laurent Modolo authored 4 years ago
  
  71eb3162
- bwa: fix bug :46 · 801d4f6a
  Laurent Modolo authored 4 years ago
  
  801d4f6a
- bwa: fix previous commit · e801efee
  Laurent Modolo authored 4 years ago
  
  e801efee
- bwa: conditional definition of the library tag · 70a181f4
  Laurent Modolo authored 4 years ago
  
  70a181f4
- bwa: fix bam tag format · 0db3382c
  Laurent Modolo authored 4 years ago
  
  0db3382c
- Docker: add star 2.5.3 · e66e20ab
  Laurent Modolo authored 4 years ago
  
  e66e20ab
- gatk4: make gvcf_genotyping emit vcf.gz files · e3b5bc65
  Laurent Modolo authored 4 years ago
  
  e3b5bc65
- Docker: g2gtools, add procps for nextflow · 8ea08355
  Laurent Modolo authored 4 years ago
  
  8ea08355
- Docker: fix g2gtools dependencies · bc5cc99e
  Laurent Modolo authored 4 years ago
  
  bc5cc99e
- .gitignore: ingore vscode file · 823a6c48
  Laurent Modolo authored 4 years ago
  
  823a6c48
- g2gtools: add incorporate_snp and incorporate_indel processes · b23c5e41
  Laurent Modolo authored 4 years ago
  
  b23c5e41
- Docker: g2gtools add pysam dependency · 308f6c25
  Laurent Modolo authored 4 years ago
  
  308f6c25
- g2gtools: add vci_build process · c251a789
  Laurent Modolo authored 4 years ago
  
  c251a789
Mar 11, 2021
- gatk4: fix option for Haplotypecaller · 3ea4e9e6
  Laurent Modolo authored 4 years ago
  
  3ea4e9e6
Mar 10, 2021
- gatk4: change recalibrate_snp to pair recall_table with BAM · 913a420c
  Laurent Modolo authored 4 years ago
  
  913a420c
- gatk4: switch PrintRead to ApplyBQSR · f4e08eb8
  Laurent Modolo authored 4 years ago
  
  f4e08eb8
- gatk4: add vcf indexing for BaseRecalibartor · 2820a500
  Laurent Modolo authored 4 years ago
  
  2820a500
- gatk4: fix BaseRecalibrator params · 1edca65d
  Laurent Modolo authored 4 years ago
  
  1edca65d
- gatk4: fix VariantFiltration params · 6d69470a
  Laurent Modolo authored 4 years ago
  
  6d69470a
- gatk4: update SelectVariants options · b5fa57a6
  Laurent Modolo authored 4 years ago
  
  b5fa57a6
- gatk4: fix SelectVariants cmd (remove -T) · 93c9b2e9
  Laurent Modolo authored 4 years ago
  
  93c9b2e9
Mar 09, 2021
- gatk4: remove spark... · b18b1efe
  Laurent Modolo authored 4 years ago
  
  b18b1efe
- gatk4: fix java-options · 8e3c7bf4
  Laurent Modolo authored 4 years ago
  
  8e3c7bf4
- gatk4: change -o to -O · 342d3265
  Laurent Modolo authored 4 years ago
  
  342d3265
- gatk4: fix spark config · b2d82f21
  Laurent Modolo authored 4 years ago
  
  b2d82f21
- gatk4: change -nct to --spark-master option · c0aef2ef
  Laurent Modolo authored 4 years ago
  
  c0aef2ef
Mar 08, 2021
- gatk4: remove unnecessary -T option · 021ace34
  Laurent Modolo authored 4 years ago
  
  021ace34
- gatk4: try to fix task memory parsing · 2d1951f6
  Laurent Modolo authored 4 years ago
  
  2d1951f6
- gatk4: add G unit to xmx params · 986ed55b
  Laurent Modolo authored 4 years ago
  
  986ed55b
- gatk4: add xmx_memory parsing for every process · ca0ecd54
  Laurent Modolo authored 4 years ago
  
  ca0ecd54
- docker: add r 4.0.3 · ead3fe96
  Laurent Modolo authored 4 years ago
  
  ead3fe96
- gatk4: fix typo :264 · 61d6bb79
  Laurent Modolo authored 4 years ago
  
  61d6bb79
- gatk4: change Xmx option parsing · 8818f78d
  Laurent Modolo authored 4 years ago
  
  8818f78d
Mar 05, 2021
- nf_modules: add gatk4 · bea9b094
  Laurent Modolo authored 4 years ago
  
  bea9b094
- nextflow.config: remove space in memory declaration · 799be6b8
  Laurent Modolo authored 4 years ago
  
  799be6b8
Mar 02, 2021
- macs2: caputre *_peaks.xls for multiqc report · 19ff2662
  Laurent Modolo authored 4 years ago
  
  19ff2662
Feb 25, 2021
- bwa: add quote surrounding -R option · 97953ba2
  Laurent Modolo authored 4 years ago
  
  97953ba2
- bwa: fix bwa_mem_R call · ade97af3
  Laurent Modolo authored 4 years ago
  
  ade97af3
- bwa: add params.bwa_mem_R variable · 449693e2
  Laurent Modolo authored 4 years ago
  
  449693e2
Feb 24, 2021
- picard: fix output name of index_fasta · 40ebfabd
  Laurent Modolo authored 4 years ago
  
  40ebfabd