Commits · 46c1f9f2f00102f117bd8615648cfafe820c698f · cbourgeo / nextflow

23 Oct, 2018 17 commits
- BWA: nf update psmn config · 46c1f9f2
  Laurent Modolo authored Oct 23, 2018
  
  46c1f9f2
- sambamba: nf update psmn config · 14164fee
  Laurent Modolo authored Oct 23, 2018
  
  14164fee
- Bowtie2: nf update config for psmn · 2973fe82
  Laurent Modolo authored Oct 23, 2018
  
  2973fe82
- RSEM: nf update indexing config for psmn · c95c7e0c
  Laurent Modolo authored Oct 23, 2018
  
  c95c7e0c
- nf module: update executor from psmn to sge · 9fdc0424
  Laurent Modolo authored Oct 23, 2018
  
  9fdc0424
- MultiQC: nf update psmn config · 1900998a
  Laurent Modolo authored Oct 23, 2018
  
  1900998a
- RSEM: nf update psmn config · 68aa07a8
  Laurent Modolo authored Oct 23, 2018
  
  68aa07a8
- UrQt: cleanup old config · c34e43a8
  Laurent Modolo authored Oct 23, 2018
  
  c34e43a8
- MUSIC: update psmn config · 86a3e164
  Laurent Modolo authored Oct 23, 2018
  
  86a3e164
- nf config file update nf syntax for process · 3e2c83f3
  Laurent Modolo authored Oct 23, 2018
  
  3e2c83f3
- change occurences of sge into psmn · cdb93acd
  Laurent Modolo authored Oct 23, 2018
  
  cdb93acd
- nf config: rename sge to psmn · fa486dc6
  Laurent Modolo authored Oct 23, 2018
  
  fa486dc6
- TP_experimental_biologists.md: update with new nf path · 978f7576
  Laurent Modolo authored Oct 23, 2018
  
  978f7576
- Kallisto: update nf config for PSMN · 35e3593b
  Laurent Modolo authored Oct 23, 2018
  
  35e3593b
- BEDtools: update nf config file for PSMN · c1446208
  Laurent Modolo authored Oct 23, 2018
  
  c1446208
- UrQt: update nf config file for the PSMN · e8805ca1
  Laurent Modolo authored Oct 23, 2018
  
  e8805ca1
- cutadapt: update nf config files for the PSMN · 0e1bad5e
  Laurent Modolo authored Oct 23, 2018
  
  0e1bad5e
16 Oct, 2018 5 commits
- Merge branch 'dev' · c5a7aa0f
  Laurent Modolo authored Oct 16, 2018
  
  c5a7aa0f
- README.md: add new tools to the table · 03283317
  Laurent Modolo authored Oct 16, 2018
  
  03283317
- Merge branch 'Delattre/JU28_59vs17_SNP-master' into dev to get BWA GATK... · a2f9dcc6
  Laurent Modolo authored Oct 16, 2018
```
Merge branch 'Delattre/JU28_59vs17_SNP-master' into dev to get BWA GATK sambamba samblaster and bcftools
```
  a2f9dcc6
- restore bowtie2 from dev · 3ecf28b8
  Laurent Modolo authored Oct 16, 2018
  
  3ecf28b8
- rm SNP_calling scripts · 315a6d3a
  Laurent Modolo authored Oct 16, 2018
  
  315a6d3a
12 Oct, 2018 2 commits
- 1_JU28_59vs17_SNP_calling.sh: change genome ref for intersect_SNP.R · 4beda1d1
  Laurent Modolo authored Oct 12, 2018
  
  4beda1d1
- intersect_SNP.R: fix getting sequences part · 1ca66529
  Laurent Modolo authored Oct 12, 2018
  
  1ca66529
11 Oct, 2018 4 commits
- SNP_calling.config: fix module load for SGE · ef2f3fe2
  Laurent Modolo authored Oct 11, 2018
  
  ef2f3fe2
- 1_JU28_59vs17_SNP_calling.sh: add analysis of final_assembly.fasta · 4aec8f08
  Laurent Modolo authored Oct 11, 2018
  
  4aec8f08
- 1_JU28_59vs17_SNP_calling.sh: add PSMN cmd · 741269e6
  Laurent Modolo authored Oct 11, 2018
  
  741269e6
- SNP_calling.config: add bioawk for sge · ea17baf9
  Laurent Modolo authored Oct 11, 2018
  
  ea17baf9
10 Oct, 2018 2 commits
- SNP_calling.config: rename some module to load · ec7d1b21
  Laurent Modolo authored Oct 10, 2018
  
  ec7d1b21
- SNP_calling.nf: add SGE config · 3d210a36
  Laurent Modolo authored Oct 10, 2018
  
  3d210a36
09 Oct, 2018 4 commits
- 1_JU28_59vs17_SNP_calling.sh: test of blast · 5d990d32
  Laurent Modolo authored Oct 09, 2018
  
  5d990d32
- SNP_calling.nf: cleanup gatk code · b85258ad
  Laurent Modolo authored Oct 09, 2018
  
  b85258ad
- 1_JU28_59vs17_SNP_calling.sh: blast of 5S on the assembly · b6551f07
  Laurent Modolo authored Oct 09, 2018
  
  b6551f07
- intersect_SNP.R: add enzyme selection · f0432019
  Laurent Modolo authored Oct 09, 2018
  
  f0432019
08 Oct, 2018 6 commits
- SNP_calling.nf: fix format · 16f01d2f
  Laurent Modolo authored Oct 08, 2018
  
  16f01d2f
- bcftools: add docker file and rm from SAMtools · 12be019b
  Laurent Modolo authored Oct 08, 2018
  
  12be019b
- 1_JU28_59vs17_SNP_calling.R: add SNP alert · a79c7a67
  Laurent Modolo authored Oct 08, 2018
  
  a79c7a67
- intersect_SNP.R: remove print · af6eda55
  Laurent Modolo authored Oct 08, 2018
  
  af6eda55
- intersect_SNP.R: sort results by AF · df87f670
  Laurent Modolo authored Oct 08, 2018
  
  df87f670
- 1_JU28_59vs17_SNP_calling.R: add SNP filtering step · 7bf6ea38
  Laurent Modolo authored Oct 08, 2018
  
  7bf6ea38