Commits · 2dcade8937fb9a81eac154d3610b018339e9e5da · Xavier Grand / ChIPster · GitLab

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Jun 17, 2021
- gatk4: working variant calling pipeline · 2dcade89
  Laurent Modolo authored 3 years ago
  
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  2dcade89
Jun 02, 2021
- gatk4: fix include path · 179127d0
  Laurent Modolo authored 3 years ago
  
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  179127d0
- gatk4: fix include path · 78ed7b01
  Laurent Modolo authored 3 years ago
  
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  78ed7b01
- fix emit: for named workflow · 92e0e00a
  Laurent Modolo authored 3 years ago
  
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  92e0e00a
- add example of variant calling with gatk4 · e363dd6f
  Laurent Modolo authored 3 years ago
  
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  e363dd6f
Jun 01, 2021
- gatk4: first version of new variant calling workflow · 94772e16
  Laurent Modolo authored 3 years ago
  
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  94772e16
Apr 21, 2021
- gatk4: match gatk3 params.* · 86cd76b3
  Laurent Modolo authored 3 years ago
  
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  86cd76b3
Apr 14, 2021
- nf_modules: update module from g2gtools to multiqc to match the CONTRIBUTING.md · 8afe54bb
  Laurent Modolo authored 3 years ago
  
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  8afe54bb
Apr 08, 2021
- nf_modules: add params.<process_names> for each process · 4a7355a2
  Laurent Modolo authored 3 years ago
  
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  4a7355a2
Mar 16, 2021
- gatk4: fix gvcf_genotyping variable :199 · 106ff35f
  Laurent Modolo authored 4 years ago
  
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  106ff35f
- gatk4: change output to avoid using file_id var as it can be a dict · e0b5c50b
  Laurent Modolo authored 4 years ago
  
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  e0b5c50b
Mar 12, 2021
- gatk4: make gvcf_genotyping emit vcf.gz files · e3b5bc65
  Laurent Modolo authored 4 years ago
  
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  e3b5bc65
Mar 11, 2021
- gatk4: fix option for Haplotypecaller · 3ea4e9e6
  Laurent Modolo authored 4 years ago
  
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  3ea4e9e6
Mar 10, 2021
- gatk4: change recalibrate_snp to pair recall_table with BAM · 913a420c
  Laurent Modolo authored 4 years ago
  
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  913a420c
- gatk4: switch PrintRead to ApplyBQSR · f4e08eb8
  Laurent Modolo authored 4 years ago
  
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  f4e08eb8
- gatk4: add vcf indexing for BaseRecalibartor · 2820a500
  Laurent Modolo authored 4 years ago
  
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  2820a500
- gatk4: fix BaseRecalibrator params · 1edca65d
  Laurent Modolo authored 4 years ago
  
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  1edca65d
- gatk4: fix VariantFiltration params · 6d69470a
  Laurent Modolo authored 4 years ago
  
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  6d69470a
- gatk4: update SelectVariants options · b5fa57a6
  Laurent Modolo authored 4 years ago
  
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  b5fa57a6
- gatk4: fix SelectVariants cmd (remove -T) · 93c9b2e9
  Laurent Modolo authored 4 years ago
  
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  93c9b2e9
Mar 09, 2021
- gatk4: remove spark... · b18b1efe
  Laurent Modolo authored 4 years ago
  
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  b18b1efe
- gatk4: fix java-options · 8e3c7bf4
  Laurent Modolo authored 4 years ago
  
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  8e3c7bf4
- gatk4: change -o to -O · 342d3265
  Laurent Modolo authored 4 years ago
  
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  342d3265
- gatk4: fix spark config · b2d82f21
  Laurent Modolo authored 4 years ago
  
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  b2d82f21
- gatk4: change -nct to --spark-master option · c0aef2ef
  Laurent Modolo authored 4 years ago
  
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  c0aef2ef
Mar 08, 2021
- gatk4: remove unnecessary -T option · 021ace34
  Laurent Modolo authored 4 years ago
  
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  021ace34
- gatk4: try to fix task memory parsing · 2d1951f6
  Laurent Modolo authored 4 years ago
  
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  2d1951f6
- gatk4: add G unit to xmx params · 986ed55b
  Laurent Modolo authored 4 years ago
  
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  986ed55b
- gatk4: add xmx_memory parsing for every process · ca0ecd54
  Laurent Modolo authored 4 years ago
  
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  ca0ecd54
- gatk4: fix typo :264 · 61d6bb79
  Laurent Modolo authored 4 years ago
  
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  61d6bb79
- gatk4: change Xmx option parsing · 8818f78d
  Laurent Modolo authored 4 years ago
  
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  8818f78d
Mar 05, 2021
- nf_modules: add gatk4 · bea9b094
  Laurent Modolo authored 4 years ago
  
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  bea9b094
Feb 17, 2021
- gatk3: add new processes · 1207cdab
  Laurent Modolo authored 4 years ago
  
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  1207cdab
- gatk3: fix variant calling · eddc374c
  Laurent Modolo authored 4 years ago
  
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  eddc374c
Feb 15, 2021
- typo in gatk3 to DSL2 · 23755281
  Laurent Modolo authored 4 years ago
  
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  23755281
- add gatk3 to DSL2 · 4a115a8a
  Laurent Modolo authored 4 years ago
  
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  4a115a8a