Commits · v2.3 · genotoul-bioinfo / metagWGS

Sep 16, 2022
- Merge branch 'devel' · ce22113d
  VIENNE MAINA authored 2 years ago
  
  v2.3
  
  ce22113d
- Update docs/installation.md · 2bccaa48
  VIENNE MAINA authored 2 years ago
  
  2bccaa48
- Merge branch 'devel' · bf0a222b
  VIENNE MAINA authored 2 years ago
  
  Conflicts: README.md docs/Pipeline.png docs/Pipeline.svg nextflow.config
  bf0a222b
- Merge branch 'binning' into devel · 12070361
  VIENNE MAINA authored 2 years ago
  
  12070361
- Merge branch 'binning' into devel · efc6b024
  VIENNE MAINA authored 2 years ago
  
  Conflicts: README.md conf/functional_test.config docs/README.md docs/installation.md docs/usage.md docs/use_case.md functional_tests/README.md functional_tests/expected_processes/expected_processes_sr.tsv functional_tests/expected_processes/expected_processes_sr_assembly.tsv functional_tests/expected_processes/expected_processes_sr_flowcell.tsv functional_tests/test_download.config main.nf modules/fastqc.nf modules/kaiju.nf subworkflows/01_clean_qc.nf subworkflows/02_assembly.nf
  efc6b024
- Update binning.yml · 6aed36c5
  Jean Mainguy authored 2 years ago
  
  6aed36c5
- Update processes tests for SR · ba4064b4
  VIENNE MAINA authored 2 years ago
  
  ba4064b4
- Fix kaiju module · 547aff6d
  VIENNE MAINA authored 2 years ago
  
  547aff6d
- Delete singularity recipe for eggnog · 13698e2f
  VIENNE MAINA authored 2 years ago
  
  13698e2f
- remove index column in top taxon file · 53ed9d73
  Jean Mainguy authored 2 years ago
  
  53ed9d73
Sep 15, 2022
- modify samtools view -f 2 by samtools fastq -s singletons.fastq.gz · b7d45efb
  DARBOT Vincent authored 2 years ago
  
  b7d45efb
- Test gtdbtk bank · f162214f
  VIENNE MAINA authored 2 years ago
  
  f162214f
- Replace --binning_cross_alignment "none" by "individual" · 31531442
  VIENNE MAINA authored 2 years ago
  
  31531442
Sep 14, 2022
- Add description for top taxon affiliation file · 8ab4c09d
  Jean Mainguy authored 2 years ago
  
  #185
  8ab4c09d
- Update .gitlab-ci.yml file · fc1fbb13
  VIENNE MAINA authored 2 years ago
  
  fc1fbb13
Sep 13, 2022
- assets/multiqc/bins_abundances_header.txt · 7ea738df
  DARBOT Vincent authored 2 years ago
  
  7ea738df
Sep 12, 2022
- add 'samtools view -f 0x2' in order to discard unmapped mate paired read · a057a043
  DARBOT Vincent authored 2 years ago
  
  a057a043
Sep 09, 2022
- use case not up to date · 1e023582
  Claire Hoede authored 2 years ago
  
  1e023582
- use_case not up to date · 30473057
  Claire Hoede authored 2 years ago
  
  30473057
- remove conda profile part because it's not working anymore · 085f42e6
  Claire Hoede authored 2 years ago
  
  085f42e6
- README.md remove skip for cleaning mention · dcbbd2d4
  Claire Hoede authored 2 years ago
  
  dcbbd2d4
- tar -xvzf instead gunzip · 272549be
  Claire Hoede authored 2 years ago
  
  272549be
- Update path toward DB · 234626d8
  Claire Hoede authored 2 years ago
  
  234626d8
- Update path toward DB · 93b83d69
  Claire Hoede authored 2 years ago
  
  93b83d69
- changes the name of the archive containing the databanks · bc6fb8aa
  Claire Hoede authored 2 years ago
  
  bc6fb8aa
Sep 08, 2022
- add top n taxon variable into the title. · 477daf92
  Jean Mainguy authored 2 years ago
  
  477daf92
- correct typo in plot title from previous correction. · af696e14
  Jean Mainguy authored 2 years ago
  
  af696e14
- correct typo in plot title. · c8c470e1
  Jean Mainguy authored 2 years ago
  
  c8c470e1
- Update conf/functional_test.config · 382923a1
  VIENNE MAINA authored 2 years ago
  
  382923a1
- Update eggnog mapper version to 2.1.9 · 2d79dd24
  VIENNE MAINA authored 2 years ago and VIENNE MAINA committed 2 years ago
  
  2d79dd24
- Update publishDir pattern · f219c49d
  VIENNE MAINA authored 2 years ago and VIENNE MAINA committed 2 years ago
  
  f219c49d
- correct table header · 04db6284
  DARBOT Vincent authored 2 years ago
  
  04db6284
Sep 07, 2022
- Modify filter on heatmap to display the 30 most abundant genomes between all samples · ac5a1a92
  DARBOT Vincent authored 2 years ago
  
  ac5a1a92
- add header to bins dereplicated stats table · a6a6b045
  DARBOT Vincent authored 2 years ago
  
  a6a6b045
- Update docs/use_case.md · 7a614bbb
  DARBOT Vincent authored 2 years ago
  
  7a614bbb
- First modifications of docs/use_case.md · c402f7a1
  DARBOT Vincent authored 2 years ago
  
  c402f7a1
- Update README.md · 88e56da4
  Claire Hoede authored 2 years ago
  
  88e56da4
- change order custom contents multiqc · 9d3eccdb
  DARBOT Vincent authored 2 years ago
  
  9d3eccdb
- correction of docs/08_binning.png · e1ff7962
  DARBOT Vincent authored 2 years ago
  
  e1ff7962
- correction of docs/08_binning.png · c6b00c78
  DARBOT Vincent authored 2 years ago
  
  c6b00c78