Commits · b3eeb7251cd99a79f0446630b3b0aed65bfa44fb · TRANSVIHMI / nfernandez / GeVarLi

Nov 27, 2024
- Doc: create CI web pages test · cb411735
  nicolas.fernandez_ird.fr authored 4 months ago
  
  cb411735
- Doc: Edit README.md · f5836637
  nicolas.fernandez_ird.fr authored 4 months ago
  
  f5836637
Nov 19, 2024
- Feat: remove LoFreq from variant caller option · d6d05ed4
  nicolas.fernandez_ird.fr authored 5 months ago
  
  d6d05ed4
Nov 15, 2024
- Feat: add Chikungunya-virus_HM-045817-1 reference genome · 715c2127
  nicolas.fernandez_ird.fr authored 5 months ago
  
  715c2127
Oct 22, 2024
- Fix: change old paths for update, init and version, form miniconda3 to miniforge3 · a62df477
  nicolas.fernandez_ird.fr authored 6 months ago
  
  a62df477
Aug 05, 2024
- Doc: update README.md · c97d967e
  nicolas.fernandez_ird.fr authored 8 months ago
  
  c97d967e
- Doc: update gevarli rulegraphe and filegraph png · 70439065
  nicolas.fernandez_ird.fr authored 8 months ago
  
  70439065
Aug 02, 2024
- Feat: new module, bamclipper · d0116935
  nicolas.fernandez_ird.fr authored 8 months ago
  
  d0116935
Jul 03, 2024
- Update: workflow-base with Snakemake 8.4.6 to 8.14.0 ; Mamba 1.5.6 to 1.5.8 ;... · 703d10cd
  nicolas.fernandez_ird.fr authored 9 months ago
  
  Update: workflow-base with Snakemake 8.4.6 to 8.14.0 ; Mamba 1.5.6 to 1.5.8 ; Yq 3.2.3 to 3.4.3 ; Graphviz 9.0.0 to 11.0.0
  703d10cd
Jul 02, 2024
- Fix: Measles virus genome file names sapce removed · adbc0ab8
  nicolas.fernandez_ird.fr authored 9 months ago
  
  adbc0ab8
- Feat: Add 3 12S reference · cdb0ee1c
  nicolas.fernandez_ird.fr authored 9 months ago
  
  cdb0ee1c
- Feat: Add 6 Measles virus (MeV) references · d5a44416
  nicolas.fernandez_ird.fr authored 9 months ago
  
  d5a44416
Apr 29, 2024
- Fix: Genomes Ref Header Names · cc49a205
  nicolas.fernandez_ird.fr authored 11 months ago
  
  cc49a205
Apr 05, 2024
- rename Loaloa as QC Loaloa · 6be3352d
  nicolas.fernandez_ird.fr authored 1 year ago
  
  6be3352d
Mar 15, 2024
- Fix: remove rule 'lofreq_alnqual' · 225e34b5
  nicolas.fernandez_ird.fr authored 1 year ago
  
  225e34b5
Feb 20, 2024
- Doc: Update version where needed · ffc71408
  nicolas.fernandez_ird.fr authored 1 year ago
  
  ffc71408
Feb 08, 2024
- Update: multiqc to 1.19 (with Pandoc) · 2ca2b9b6
  nicolas.fernandez_ird.fr authored 1 year ago
  
  2ca2b9b6
- Feature: add ivar.tsv 2 .vcf files · 32467329
  nicolas.fernandez_ird.fr authored 1 year ago
  
  32467329
Feb 02, 2024
- Add iVar as variant caller · a028d833
  nicolas.fernandez_ird.fr authored 1 year ago
  
  a028d833
Jan 19, 2024
- Update Nextclade to v.3.0.0 · 7b3c922c
  nicolas.fernandez_ird.fr authored 1 year ago
  
  7b3c922c
Oct 26, 2023
- Add network check · d941837f
  nicolas.fernandez_ird.fr authored 1 year ago
  
  d941837f
Sep 04, 2023
- doc: fix 'how to' update nextclade · 170043f9
  nicolas.fernandez_ird.fr authored 1 year ago
  
  170043f9
Jul 19, 2023
- docs: add download procedure help picture · 608baf16
  nicolas.fernandez_ird.fr authored 1 year ago
  
  View commits for tag v.2023.06_1.1 v.2023.06_1.1
  
  608baf16
Jun 26, 2023
- Update Nextclade to 2.14.0 and database (for Linux users) · 5f935cb3
  nicolas.fernandez_ird.fr authored 1 year ago
  
  5f935cb3
Jun 23, 2023
- Update Nextclade to 2.14.0 and database (for MacOSx users · c9051aa7
  nicolas.fernandez_ird.fr authored 1 year ago
  
  c9051aa7
Apr 04, 2023

Replace Soft-Clipping (Bamclipper) with Hard-Clipping (Cutadapt) ; Add... · 6ee06427

nicolas.fernandez_ird.fr authored 2 years ago

Replace Soft-Clipping (Bamclipper) with Hard-Clipping (Cutadapt) ; Add Varicella Reference ; Change Yaml parsing for Yq tool ; Config Yaml allow multiple min_cov / aligner / reference (soon) ; Nextclade Updade to 2.13.1

6ee06427

Mar 01, 2023
- Update GeVarLi env ver.2023.02 with Nextclade ver. 2.11.0 (up from 2.9.1) · 83bbe212
  nicolas.fernandez_ird.fr authored 2 years ago
  
  83bbe212
Jan 17, 2023
- Update README.md for v2023.01 · 81f8ceca
  nicolas.fernandez_ird.fr authored 2 years ago
  
  81f8ceca
Jan 09, 2023
- nextclade databases update · f955668e
  nicolas.fernandez_ird.fr authored 2 years ago
  
  View commits for tag v.2023.01 v.2023.01
  
  f955668e
Dec 22, 2022
- Add Pandoc to MultiQC env to pdf export · 8ca70403
  nicolas.fernandez_ird.fr authored 2 years ago
  
  8ca70403
Dec 21, 2022
- Add Pandoc to MultiQC env to pdf export · a6dbac9c
  nicolas.fernandez_ird.fr authored 2 years ago
  
  a6dbac9c
Nov 14, 2022
- Add SARS-CoV-2 fastq data test in resources · 9b47ef15
  Nicolas FERNANDEZ NUÑEZ authored 2 years ago
  
  9b47ef15
Oct 06, 2022
- Remove bedpe generation · 8127fc50
  Nicolas FERNANDEZ NUÑEZ authored 2 years ago
  
  8127fc50
Sep 30, 2022
- Add features like genomes indexing and bamclipping · 1373c03f
  Nicolas FERNANDEZ NUÑEZ authored 2 years ago
  
  1373c03f
Jul 27, 2022
- Test .gitignore · 8124c4a9
  Nicolas FERNANDEZ NUÑEZ authored 2 years ago
  
  8124c4a9
Jul 22, 2022
- Update Nextclade to 2.3.0 from 1.11.0 conda env · 94557538
  Nicolas FERNANDEZ NUÑEZ authored 2 years ago
  
  94557538
Mar 25, 2022
- Update Nextclade database to 1.11.0, report Pangolin lineage & correct 'iuapc'... · 623f0c50
  Nicolas FERNANDEZ NUÑEZ authored 3 years ago
  
  Update Nextclade database to 1.11.0, report Pangolin lineage & correct 'iuapc' to 'iupac' typo error
  623f0c50
Feb 01, 2022
- Updating Nextclade env and databases from 1.9.0 to 1.10.1 · ab2fcc74
  Nicolas FERNANDEZ NUÑEZ authored 3 years ago
  
  ab2fcc74
Jan 18, 2022
- Adding nextclade assignation and updating README.md · 1e1271a6
  Nicolas FERNANDEZ NUÑEZ authored 3 years ago
  
  1e1271a6
- Adding nextclade assignation and updating README.md · 1ab7dc5d
  Nicolas FERNANDEZ NUÑEZ authored 3 years ago
  
  1ab7dc5d