Commits · 9f7c81b715e901b05257c551cc39eb25ffb38801 · LBMC / nextflow · GitLab

Snippets Groups Projects

Oct 07, 2021
- samtools: fix process name :79 · 8f94a832
  Laurent Modolo authored 3 years ago
  
  Verified
  
  8f94a832
- samtools: add rm_from_bam process · e4d6d7ab
  Laurent Modolo authored 3 years ago
  
  Verified
  
  e4d6d7ab
Oct 06, 2021
- samtools: fix bug :21 · 7286daef
  Laurent Modolo authored 3 years ago
  
  Verified
  
  7286daef
- samtools: add gzip for samtools faidx · d5cacb23
  Laurent Modolo authored 3 years ago
  
  Verified
  
  d5cacb23
Jun 04, 2021
- cleanup DSL1 test.sh · 2150d981
  Laurent Modolo authored 3 years ago
  
  Verified
  
  2150d981
- switcth to nextflow DSL2 · cc2d49f6
  Laurent Modolo authored 3 years ago
  
  Verified
  
  cc2d49f6
Apr 27, 2021
- nf_modules: minors fix in deeptools and samtools · c52ab0e7
  Laurent Modolo authored 3 years ago
  
  Verified
  
  c52ab0e7
Apr 26, 2021
- samtools: fix split_bam @ option · 1f25c4c5
  Laurent Modolo authored 3 years ago
  
  Verified
  
  1f25c4c5
Apr 15, 2021
- samtools: update publishDir directives · c6944a8e
  Laurent Modolo authored 4 years ago
  
  Verified
  
  c6944a8e
- nf_modules: fix bug in variable names for samtools and bwa · c75f1dda
  Laurent Modolo authored 4 years ago
  
  Verified
  
  c75f1dda
- nf_modules: update last main.nf to change in CONTRIBUTING.md · fdb5acb8
  Laurent Modolo authored 4 years ago
  
  Verified
  
  fdb5acb8
Apr 14, 2021
- samtools: update to follow CONTRIBUTING.md · 84daa858
  Laurent Modolo authored 4 years ago
  
  Verified
  
  84daa858
Mar 16, 2021
- samtools: fix input for multiqc process · 15bb2a0a
  Laurent Modolo authored 4 years ago
  
  Verified
  
  15bb2a0a
- samtools: fix output for multiqc process · ce6cb60b
  Laurent Modolo authored 4 years ago
  
  Verified
  
  ce6cb60b
- samtools: add process to rename files for multiqc · 309f80d7
  Laurent Modolo authored 4 years ago
  
  Verified
  
  309f80d7
Feb 22, 2021
- picard: improve picard index output · 2fde78ba
  Laurent Modolo authored 4 years ago
  
  Verified
  
  2fde78ba
- samtools: fix merge_multi_bam · 493aaa15
  Laurent Modolo authored 4 years ago
  
  Verified
  
  493aaa15
- samtools: fix merge_multi_bam · aa838665
  Laurent Modolo authored 4 years ago
  
  Verified
  
  aa838665
Feb 17, 2021
- samtools: modify output name of merge_multi_bam · cd23e1e3
  Laurent Modolo authored 4 years ago
  
  Verified
  
  cd23e1e3
- samtools: add process to merge multiple bam · ff5c7a24
  Laurent Modolo authored 4 years ago
  
  Verified
  
  ff5c7a24
Feb 15, 2021
- add gatk3 to DSL2 · 4a115a8a
  Laurent Modolo authored 4 years ago
  
  Verified
  
  4a115a8a
- update picard samtools and bwa for DSL2 · 7a17de40
  Laurent Modolo authored 4 years ago
  
  Verified
  
  7a17de40
Feb 03, 2021
- samtools: main.nf clarify bam_index output1 · b9d4fdda
  Laurent Modolo authored 4 years ago
  
  Verified
  
  b9d4fdda
- samtools: test for indexing · ed50e0a0
  Laurent Modolo authored 4 years ago
  
  Verified
  
  ed50e0a0
Jan 29, 2021
- samtools: change file_id to bam.simpleName · 0dff7e33
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  0dff7e33
- docker: add samtools v1.11 · 962ac77e
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  962ac77e
- samtools: fix flagstats cmd · ebb5cb65
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  ebb5cb65
- samtools: change label for bam_stats · 42f56bde
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  42f56bde
- samtools: add bam_stats process · a4d4bdb9
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  a4d4bdb9
Jan 25, 2021
- samtools: fix filter_bam_mapped · e3a42082
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  e3a42082
- samtools: fix catched bams names · 9f34d846
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  9f34d846
- samtools: fix samtools version · a8e8560a
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  a8e8560a
- fix input and output for bedtools and samtools · 8bebb4a1
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  8bebb4a1
- samtools: nf_module add mapped and unmapped filter · de331fa7
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  de331fa7
Jan 22, 2021
- nf_modules: add samtools DSL2 · 3de89ded
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  3de89ded
Apr 27, 2020
- remove copying for psmn config · 87c79ae2
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  87c79ae2
Apr 20, 2020
- nf_modules: disable scratch for psmn · 8d47aa31
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  8d47aa31
- nf_modules: switch psmn to singularity · 670315f5
  Laurent Modolo authored 4 years ago
  
  Unverified
  
  670315f5
Apr 17, 2020
- update psmn config to new queues · c116038b
  Laurent Modolo authored 5 years ago
  
  Unverified
  
  c116038b
Nov 28, 2019
- *.config: fix singularity cacheDir path for in2p3 · 30b52060
  Laurent Modolo authored 5 years ago
  
  Unverified
  
  30b52060