Commits · master · genotoul-bioinfo / metagWGS

20 Jun, 2022 2 commits
- Replace Pipeline.png · 78149fa5
  Claire Hoede authored Jun 20, 2022
  
  78149fa5
- Replace Pipeline.svg · 6ed2d14c
  Claire Hoede authored Jun 20, 2022
  
  6ed2d14c
14 Jun, 2022 1 commit
- Correct skip parameter for assembly filtering · 989ac593
  Claire Hoede authored Jun 14, 2022
  
  989ac593
10 Jun, 2022 1 commit
- Update metagWGS version · cd1fafc8
  Claire Hoede authored Jun 10, 2022
  
  cd1fafc8
30 May, 2022 4 commits
- Merge branch 'revert-b0745a37' into 'master' · cb5a6cac
  Jean Mainguy authored May 30, 2022
```
Revert "Merge branch 'jean.mainguy-master-patch-09797' into 'master'"

See merge request !18
```
  cb5a6cac
- Revert "Merge branch 'jean.mainguy-master-patch-09797' into 'master'" · e324022c
  Jean Mainguy authored May 30, 2022
```
This reverts merge request !17
```
  e324022c
- Merge branch 'jean.mainguy-master-patch-09797' into 'master' · b0745a37
  Jean Mainguy authored May 30, 2022
```
add description of top taxon output added in commit 2e1644f5 #185

See merge request !17
```
  b0745a37
- add description of top taxon output added in commit 2e1644f5 #185 · 4f324f42
  Jean Mainguy authored May 30, 2022
  
  4f324f42
01 Feb, 2022 3 commits
- Merge branch 'devel' into 'master' · b44be61c
  Celine Noirot authored Feb 01, 2022
```
Devel

See merge request !16
```
  b44be61c
- Merge branch 'master' into 'devel' · c85c328e
  Jean Mainguy authored Feb 01, 2022
```
# Conflicts:
#   modules/host_filter.nf
```
  c85c328e
- fix plot issue: plot are only generated at the end. · ec2eefa6
  Jean Mainguy authored Feb 01, 2022
  
  ec2eefa6
26 Jan, 2022 2 commits
- update doc and help: add '--type' description · 5b588d44
  VIENNE MAINA authored Jan 26, 2022
  
  5b588d44
- update functional test : expected processes Hifi · 7077b531
  VIENNE MAINA authored Jan 26, 2022
  
  7077b531
25 Jan, 2022 1 commit
- add flagstat report of HiFi reads in multiqc report · a189d131
  Jean Mainguy authored Jan 25, 2022
  
  a189d131
24 Jan, 2022 3 commits
- Update host_filter.nf (replace bamtofastq by samtools fastq ) · 8335fddb
  VIENNE MAINA authored Jan 24, 2022
  
  8335fddb
- Update host_filter.nf · a72fc84c
  VIENNE MAINA authored Jan 24, 2022
  
  a72fc84c
- Update host_filter.nf (replace bamtofastq by samtools fastq ) · 97c1ff29
  VIENNE MAINA authored Jan 24, 2022
  
  97c1ff29
21 Jan, 2022 2 commits
- Update host_filter.nf · 69453c3e
  VIENNE MAINA authored Jan 21, 2022
  
  69453c3e
- Update host_filter.nf · c1241934
  VIENNE MAINA authored Jan 21, 2022
  
  c1241934
20 Jan, 2022 1 commit
- Use current paths for taxdump and accession2taxid to always use the most... · f454f4e4
  Jean Mainguy authored Jan 20, 2022
```
Use current paths for taxdump and accession2taxid to always use the most recent db available on the cluster. 
```
  f454f4e4
17 Jan, 2022 4 commits
- Update expected_processes_HiFi.tsv · 4bfe5e51
  VIENNE MAINA authored Jan 17, 2022
  
  4bfe5e51
- Merge branch 'master' of https://forgemia.inra.fr/genotoul-bioinfo/metagwgs · 16ea1dd2
  VIENNE MAINA authored Jan 17, 2022
  
  16ea1dd2
- update expected processes for HiFi · 81cc7a8e
  VIENNE MAINA authored Jan 17, 2022
  
  81cc7a8e
- take all selected hits to affiliate contigs · 60e31ed9
  Jean Mainguy authored Jan 17, 2022
  
  60e31ed9
14 Jan, 2022 9 commits
- update expected processes for short reads · 112c29c8
  VIENNE MAINA authored Jan 14, 2022
  
  112c29c8
- Update README.md · 12fc1e33
  Celine Noirot authored Jan 14, 2022
  
  12fc1e33
- update docs after merge · f9e72035
  VIENNE MAINA authored Jan 14, 2022
  
  f9e72035
- Update usage.md · d811df57
  Celine Noirot authored Jan 14, 2022
  
  d811df57
- Merge branch 'dev' into 'master' · d90c0efa
  Celine Noirot authored Jan 14, 2022
```
DSL2

Closes #108

See merge request !15
```
  d90c0efa
- Merge branch 'master' into 'dev' · 529e7714
  Celine Noirot authored Jan 14, 2022
```
# Conflicts:
#   README.md
#   docs/README.md
#   docs/installation.md
#   docs/usage.md
#   functional_tests/README.md
#   functional_tests/functions.py
#   functional_tests/launch_example.sh
#   functional_tests/main.py
#   main.nf
#   nextflow.config
```
  529e7714
- add default parameters for genotoul profile · 2b23244c
  Jean Mainguy authored Jan 14, 2022
  
  2b23244c
- Merge branch 'dev_docs' into 'dev' · 05d051e0
  Celine Noirot authored Jan 14, 2022
```
Dev docs

See merge request !14
```
  05d051e0
- update functional test to take into account new taxonomy parameters · a689edb8
  VIENNE MAINA authored Jan 14, 2022
  
  a689edb8
13 Jan, 2022 7 commits
- Merge branch 'dev_docs' of https://forgemia.inra.fr/genotoul-bioinfo/metagwgs into dev_docs · 051b92ff
  VIENNE MAINA authored Jan 13, 2022
```
Conflicts:
	functional_tests/launch_example.sh
```
  051b92ff
- update functional_tests with new profiles · ee4c12a0
  VIENNE MAINA authored Jan 11, 2022
  
  ee4c12a0
- update docs + add environement variables · 20dc1171
  VIENNE MAINA authored Jan 10, 2022
  
  20dc1171
- replace bedtools bamtofastq with samtools fastq (direct fastq.gz) · 66af6629
  VIENNE MAINA authored Jan 13, 2022
  
  66af6629
- Check gff validity (issue : check point prokka) · 04ddeaa0
  VIENNE MAINA authored Jan 11, 2022
  
  04ddeaa0
- update functional_tests with new profiles · 43329377
  VIENNE MAINA authored Jan 11, 2022
  
  43329377
- update docs + add environement variables · 828d606b
  VIENNE MAINA authored Jan 10, 2022
  
  828d606b