Commits · master · genotoul-bioinfo / metagWGS

21 Jan, 2022 1 commit
- 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 25 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
- remove diamond bank necessity when not use · 96471aed
  VIENNE MAINA authored Jan 11, 2022
  
  96471aed
- update docs + add environement variables · 29195043
  VIENNE MAINA authored Jan 10, 2022
  
  29195043
- correct host + taxonomy_dir paths · 6b4dd74d
  VIENNE MAINA authored Jan 10, 2022
  
  6b4dd74d
- correct eggnog mapper version bug while not use · 2b61f674
  VIENNE MAINA authored Jan 10, 2022
  
  2b61f674
- Merge branch 'dev_docs' of https://forgemia.inra.fr/genotoul-bioinfo/metagwgs into dev_docs · 6b5f86b5
  VIENNE MAINA authored Jan 13, 2022
  
  6b5f86b5
- replace bedtools bamtofastq with samtools fastq (direct fastq.gz) · c2523f7e
  VIENNE MAINA authored Jan 13, 2022
  
  c2523f7e
- Check gff validity (issue : check point prokka) · 69c1bb09
  VIENNE MAINA authored Jan 11, 2022
  
  69c1bb09
- update functional_tests with new profiles · e6fd319d
  VIENNE MAINA authored Jan 11, 2022
  
  e6fd319d
- remove diamond bank necessity when not use · 944d0efb
  VIENNE MAINA authored Jan 11, 2022
  
  944d0efb
- update docs + add environement variables · b8c84a53
  VIENNE MAINA authored Jan 10, 2022
  
  b8c84a53
- correct host + taxonomy_dir paths · c95e3a73
  VIENNE MAINA authored Jan 10, 2022
  
  c95e3a73
- correct eggnog mapper version bug while not use · 0fa08f53
  VIENNE MAINA authored Jan 10, 2022
  
  0fa08f53
- Merge branch 'dev_docs' of https://forgemia.inra.fr/genotoul-bioinfo/metagwgs into dev_docs · 720e6f7c
  VIENNE MAINA authored Jan 13, 2022
  
  720e6f7c
- replace bedtools bamtofastq with samtools fastq (direct fastq.gz) · 06beeb76
  VIENNE MAINA authored Jan 13, 2022
  
  06beeb76
- Check gff validity (issue : check point prokka) · aec8331d
  VIENNE MAINA authored Jan 11, 2022
  
  aec8331d
- update functional_tests with new profiles · 9311b5c4
  VIENNE MAINA authored Jan 11, 2022
  
  9311b5c4
- remove diamond bank necessity when not use · 80566ab3
  VIENNE MAINA authored Jan 11, 2022
  
  80566ab3
- update docs + add environement variables · 96af8f1f
  VIENNE MAINA authored Jan 10, 2022
  
  96af8f1f