Commits · 309f80d7bbff74aa3439908222c47d2fbae431ff · LBMC / nextflow · GitLab

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"test.nf" did not exist on "5861de5f4c39ba95d3837b1d4ace3104698c093f"

Mar 16, 2021
- samtools: add process to rename files for multiqc · 309f80d7
  Laurent Modolo authored 4 years ago
  
  309f80d7
- nexflow.config: rm sratch config for psmn · 22495331
  Laurent Modolo authored 4 years ago
  
  22495331
- g2gtools: simpler file_id structure · 17d3a31f
  Laurent Modolo authored 4 years ago
  
  17d3a31f
- g2gtools: caputre stdout sent to stderr... · d80598c8
  Laurent Modolo authored 4 years ago
  
  d80598c8
- g2gtools: capture stdout sent to stderr · 216457b0
  Laurent Modolo authored 4 years ago
  
  216457b0
- g2gtools: change file_id format · 8b41995c
  Laurent Modolo authored 4 years ago
  
  8b41995c
- gatk4: fix gvcf_genotyping variable :199 · 106ff35f
  Laurent Modolo authored 4 years ago
  
  106ff35f
- gatk4: change output to avoid using file_id var as it can be a dict · e0b5c50b
  Laurent Modolo authored 4 years ago
  
  e0b5c50b
Mar 15, 2021
- minimap2: add main.nf · 324f5505
  Laurent Modolo authored 4 years ago
  
  324f5505
- Docker: add minimap2:2.17 · 364632ef
  Laurent Modolo authored 4 years ago
  
  364632ef
Mar 12, 2021
- g2gtools: add convert process · 9c64bd7b
  Laurent Modolo authored 4 years ago
  
  9c64bd7b
- bwa: add single_end mapping · d0b4f082
  Laurent Modolo authored 4 years ago
  
  d0b4f082
- add missing pairend_end & single_end switch · c64d2dd0
  Laurent Modolo authored 4 years ago
  
  c64d2dd0
- add paired_end and single_end switch version to all implementations · e4d5b19b
  Laurent Modolo authored 4 years ago
  
  e4d5b19b
- fastp: test paired_end & single_end process · 720b1977
  Laurent Modolo authored 4 years ago
  
  720b1977
- 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
- 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