Commits · 03bcdd545034cd11a387f5adc6124c66eb071757 · genotoul-bioinfo / metagWGS

05 Jan, 2022 2 commits
- add minimap label · 03bcdd54
  Jean Mainguy authored Jan 05, 2022
  
  03bcdd54
- add gzip module needed when acc2taxid file is gziped · 99283a1b
  Jean Mainguy authored Jan 05, 2022
  
  99283a1b
29 Dec, 2021 3 commits
- Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev · b85cfd90
  Jean Mainguy authored Dec 29, 2021
  
  b85cfd90
- manage accession2taxid file gz or not · ca387e0f
  Jean Mainguy authored Dec 29, 2021
  
  ca387e0f
- remove old unused HIFI_QUAST module · ff63c2ec
  Jean Mainguy authored Dec 29, 2021
  
  ff63c2ec
20 Dec, 2021 2 commits
- Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev · 7901e952
  Celine Noirot authored Dec 20, 2021
  
  7901e952
- correct ci · 0bbccd2f
  Celine Noirot authored Dec 20, 2021
  
  0bbccd2f
17 Dec, 2021 8 commits
- Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev · add3f5cd
  Jean Mainguy authored Dec 17, 2021
  
  add3f5cd
- add hifi reads subworflow and add filtering step for hifi reads · eb95e0a4
  Jean Mainguy authored Dec 17, 2021
  
  eb95e0a4
- manual only · 1154a060
  Celine Noirot authored Dec 17, 2021
  
  1154a060
- add manual · f93a9bfc
  Celine Noirot authored Dec 17, 2021
  
  f93a9bfc
- change way ok build and deploy · d7c2f239
  Celine Noirot authored Dec 17, 2021
  
  d7c2f239
- new version · 0e818289
  Celine Noirot authored Dec 17, 2021
  
  0e818289
- Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev · fef2c774
  Celine Noirot authored Dec 17, 2021
  
  fef2c774
- Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev · 5add8d6e
  Celine Noirot authored Dec 17, 2021
  
  5add8d6e
16 Dec, 2021 9 commits
- preserve fasta file names in GLOBAL_CD_HIT to cat file in a consistent way · 58ed058e
  Jean Mainguy authored Dec 16, 2021
  
  58ed058e
- Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev · 97ab5025
  Jean Mainguy authored Dec 16, 2021
  
  97ab5025
- add sort to faciliate functional testing. · 6b2f2dda
  Jean Mainguy authored Dec 16, 2021
  
  6b2f2dda
- removed gff file from read_alignment process · 814e6a51
  MARTIN Pierre authored Dec 16, 2021
  
  814e6a51
- Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev · 1d96308c
  MARTIN Pierre authored Dec 16, 2021
  
  1d96308c
- multiple fixes · e30f00a2
  MARTIN Pierre authored Dec 16, 2021
  
  e30f00a2
- Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev · 0ff60cf3
  Jean Mainguy authored Dec 16, 2021
  
  0ff60cf3
- refactoring of aln2taxaffi. use of new_taxdump and prot.accession2taxid.FULL · cd6dd688
  Jean Mainguy authored Dec 16, 2021
  
  cd6dd688
- Update .gitlab-ci.yml · 628aee35
  MARTIN Pierre authored Dec 16, 2021
  
  628aee35
15 Dec, 2021 2 commits
- remove nogroup in fastqc hifi process because it takes too long · f81cd2d3
  Jean Mainguy authored Dec 15, 2021
  
  f81cd2d3
- add additional checking for kaiju db dir · b95a495f
  Jean Mainguy authored Dec 15, 2021
  
  b95a495f
14 Dec, 2021 1 commit
- singularity paths change · a4d66930
  MARTIN Pierre authored Dec 14, 2021
  
  a4d66930
13 Dec, 2021 6 commits
- Merge branch 'dsl2' into 'dev' · 263e2acc
  MARTIN Pierre authored Dec 13, 2021
```
Merge dsl2 in dev to finalize dsl1 to dsl2 transition

See merge request !12
```
  263e2acc
- Merge branch 'dev' into 'dsl2' · 82951f63
  MARTIN Pierre authored Dec 13, 2021
```
# Conflicts:
#   README.md
#   bin/aln2taxaffi.py
#   conf/base.config
#   conf/test_genotoul_workq.config
#   docs/README.md
#   docs/installation.md
#   docs/usage.md
#   functional_tests/main.py
#   main.nf
#   nextflow.config
```
  82951f63
- multiqc versions fix (nextflow) + multiqc_data folder published · c47901c1
  MARTIN Pierre authored Dec 13, 2021
  
  c47901c1
- Merge branch 'dsl2' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dsl2 · 49ac5e5f
  MARTIN Pierre authored Dec 13, 2021
  
  49ac5e5f
- nextflow.config singularity folder as env var · 2aef4c74
  MARTIN Pierre authored Dec 13, 2021
  
  2aef4c74
- added get_software_versions and multiqc · 0ad58879
  MARTIN Pierre authored Dec 13, 2021
  
  0ad58879
06 Dec, 2021 1 commit
- apply autopep8 · 62b9ae1b
  Jean Mainguy authored Dec 06, 2021
  
  62b9ae1b
03 Dec, 2021 3 commits
- Merge branch 'dsl2' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dsl2 · 1591727d
  MARTIN Pierre authored Dec 03, 2021
  
  1591727d
- [WIP] added get versions to MULTIQC + problem with quast report · 2aacccb4
  MARTIN Pierre authored Dec 03, 2021
  
  2aacccb4
- Update usage.md · 7e6a4aab
  Claire Hoede authored Dec 03, 2021
  
  7e6a4aab
01 Dec, 2021 1 commit
- finished hifi fastqc and databases download location · 5f899af3
  MARTIN Pierre authored Dec 01, 2021
  
  5f899af3
30 Nov, 2021 2 commits
- changed publishdir of databases when downloaded ; added fastqc to hifi reads before prokka · b24caed7
  MARTIN Pierre authored Nov 30, 2021
  
  b24caed7
- before fusion · a6dac588
  MARTIN Pierre authored Nov 30, 2021
  
  a6dac588