Commits · 36fafd898913cac7634306c3f4e088ec7ca22460 · LBMC / Delattre / JU28_59vs17_SNP · GitLab

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Oct 05, 2018
- SNP_calling.nf: add SNP_filter step · 36fafd89
  Laurent Modolo authored 6 years ago
  
  36fafd89
Oct 04, 2018
- 1_JU28_59vs17_SNP_calling.nf: fix encoding problem for genome · 58e36e9e
  Laurent Modolo authored 6 years ago
  
  58e36e9e
- Bioawk: add docker files · 3bc9cac1
  Laurent Modolo authored 6 years ago
  
  3bc9cac1
Oct 03, 2018
- 1_JU28_59vs17_SNP_calling.sh: fix tests cmd · 147563d6
  Laurent Modolo authored 6 years ago
  
  147563d6
- SNP_calling.nf: fix Mutect2 variables · d8a29f60
  Laurent Modolo authored 6 years ago
  
  d8a29f60
- SNP_calling.nf: fix collect problem · 7619538a
  Laurent Modolo authored 6 years ago
  
  7619538a
- SNP_calling.nf: last test with BWA MEM · c9fc9da5
  Laurent Modolo authored 6 years ago
  
  c9fc9da5
Oct 02, 2018
- BWA: add sambamba and samblaster to docker · 45be00ec
  Laurent Modolo authored 6 years ago
  
  45be00ec
- 1_JU28_59vs17_SNP_calling.sh: add training step analysis · 6ff24e84
  Laurent Modolo authored 6 years ago
  
  6ff24e84
Sep 26, 2018
- SNP_calling.nf: fix merge_bam · b649d2bd
  Laurent Modolo authored 6 years ago
  
  b649d2bd
Sep 25, 2018
- SNP_calling.nf: add merging step into tumor_sample and normal_sample · 60a814b3
  Laurent Modolo authored 6 years ago
  
  60a814b3
- SNP_calling.nf: sambamba change tmp dir · 209416f2
  Laurent Modolo authored 6 years ago
  
  209416f2
- SNP_calling.nf: split bam convertion and sort to avoid filling /tmp · 01aba97f
  Laurent Modolo authored 6 years ago
  
  01aba97f
Sep 24, 2018
- 1_JU28_59vs17_SNP_calling.sh: add cmd for Mutect2 · 2d8f8287
  Laurent Modolo authored 6 years ago
  
  2d8f8287
- SNP_calling.config: add docker configs · dcde6659
  Laurent Modolo authored 6 years ago
  
  dcde6659
- src/SNP_calling.nf: add Mutect2 to call SNP · 224bbd69
  Laurent Modolo authored 6 years ago
  
  224bbd69
Sep 18, 2018
- SNP_calling.nf: QC and mapping · a2f71be3
  Laurent Modolo authored 6 years ago
  
  a2f71be3
- SNP_calling.config: create pipeline conf file · 0d2b6e6c
  Laurent Modolo authored 6 years ago
  
  0d2b6e6c
- 1_JU28_59vs17_SNP_calling.sh: add sh to launch pipeline · 7efa0b93
  Laurent Modolo authored 6 years ago
  
  7efa0b93
- .gitignore: add results link · 315d032b
  Laurent Modolo authored 6 years ago
  
  315d032b
Sep 17, 2018
- GATK: add docker files · 700c50ef
  Laurent Modolo authored 6 years ago
  
  700c50ef
- sambamba: add nf files · bc91a90e
  Laurent Modolo authored 6 years ago
  
  bc91a90e
- sambamba: add Docker files · 6a540919
  Laurent Modolo authored 6 years ago
  
  6a540919
- samblaster: add nf files · 05dfb3b0
  Laurent Modolo authored 6 years ago
  
  05dfb3b0
- samblaster: add dockerfiles · ec475c5f
  Laurent Modolo authored 6 years ago
  
  ec475c5f
- BWA: add nf file for paired mapping · f40aa5d9
  Laurent Modolo authored 6 years ago
  
  f40aa5d9
Sep 14, 2018
- BWA: add docker files · a2c5d6c2
  Laurent Modolo authored 6 years ago
  
  a2c5d6c2
Sep 13, 2018
- Kallisto.nf: update report format · aac64942
  Laurent Modolo authored 6 years ago
  
  aac64942
Aug 31, 2018
- nf_modules: fix tests.sh to use local nextflow bin · 5386a286
  Laurent Modolo authored 6 years ago
  
  5386a286
- Kallisto: fix tests.sh · c43032e6
  Laurent Modolo authored 6 years ago
  
  c43032e6
Aug 29, 2018
- README.md: update MUSIC status · b49bed66
  Laurent Modolo authored 6 years ago
  
  b49bed66
- MUSIC: change read size param · 3bbe96f6
  Laurent Modolo authored 6 years ago
  
  3bbe96f6
- MUSIC: add tests.sh file to run the tests · cf94bb20
  Laurent Modolo authored 6 years ago
  
  cf94bb20
Aug 27, 2018
- training_dataset.nf: rename output · fb655dc5
  Laurent Modolo authored 6 years ago
  
  fb655dc5
- MUISC: .config: update config to match last single nf · 666d47e1
  Laurent Modolo authored 6 years ago
  
  666d47e1
- peak_calling_single.nf: select lp0 autoamtically · 51f89832
  Laurent Modolo authored 6 years ago
  
  51f89832
Aug 24, 2018
- training_dataset: add bam indexing step · 3bc22f3a
  Laurent Modolo authored 6 years ago
  
  3bc22f3a
- training_dataset.nf: fix filtering for single-end · 911287b2
  Laurent Modolo authored 6 years ago
  
  911287b2
- MUSIC: nf files for single-end data · 29267096
  Laurent Modolo authored 6 years ago
  
  29267096
- MUSIC: add samtools to the Dockerfile · 5f461c3d
  Laurent Modolo authored 6 years ago
  
  5f461c3d