Commits · v1.3 · UMR GDEC / magatt

Jan 04, 2024
- Merge branch '8-includeIsbpsMapping' into 'master' · 76bf22e3
  Helene Rimbert authored 1 year ago
  
  NEW : ISBPs extraction and mapping added in the begining of the pipeline See merge request !10
  v1.3
  
  76bf22e3
- NEW : ISBPs extraction and mapping added in the begining of the pipeline · 0fa68d60
  Helene Rimbert authored 1 year ago
  
  0fa68d60
- Add new Dockerfile · 70c7a358
  Helene Rimbert authored 1 year ago
  
  70c7a358
- Add LICENSE · a32ec486
  Helene Rimbert authored 1 year ago
  
  a32ec486
Jan 03, 2024
- Merge branch '7-gmap-rescue-on-target-only-for-genes-with-gmaprescue-file-tag' into 'master' · 36d9a8d6
  Helene Rimbert authored 1 year ago
  
  BUG : fixed bad rescue on target with gmap Closes #7 See merge request !9
  36d9a8d6
- BUG : fixed bad rescue on target with gmap · f8cbf714
  Helene Rimbert authored 1 year ago
  
  f8cbf714
Jul 05, 2023
- Merge branch 'helene.rimbert-master-patch-23301' into 'master' · 1422ec20
  Helene Rimbert authored 1 year ago
  
  Update README.md See merge request !8
  1422ec20
- Update README.md · 0df66dc8
  Helene Rimbert authored 1 year ago
  
  0df66dc8
- Merge branch 'missing_conda_rules' into 'master' · ed93ca70
  Helene Rimbert authored 1 year ago
  
  Missing conda rules See merge request !7
  v1.2
  
  ed93ca70
- UPDATE: add ne gmap management in Readme description · d0b0bfd3
  Helene Rimbert authored 1 year ago
  
  d0b0bfd3
- IMPROVE: create rulegraph and full DAG in dot format · 9c972d27
  Helene Rimbert authored 1 year ago
  
  9c972d27
- Merge branch '6-gmaprescue_global' into 'missing_conda_rules' · 2e4a5a8c
  Helene Rimbert authored 1 year ago
  
  Resolve "IMPROVE: gmap rescue in global scale" See merge request !6
  2e4a5a8c
- IMPROVE: refactor GMAP index management with parameters in config.yaml · fde7ff34
  Helene Rimbert authored 1 year ago
  
  fde7ff34
Jul 03, 2023

IMPROVE: gmapl rescue run at the end of each chomosome batch rather than for every gene · 50257cad
Helene Rimbert authored 1 year ago

50257cad

Helene Rimbert authored 1 year ago

Merge branch '5-improve-renamegffids-py-build-chromosome-map-based-on-input-gff-and-not-mapping-file' into 'missing_conda_rules'

IMPROVE: initialise chromosomeMap dict while reading input GFF

See merge request !5

e077dff2

Jun 29, 2023
- IMPROVE: initialise chromosomeMap dict while reading input GFF · 5b2c2706
  Helene Rimbert authored 1 year ago
  
  5b2c2706
Jun 21, 2023
- BUG: change keys in mappingChrom dict with target chromosome IDs instead of reference IDs · 1553a64b
  SIRVENT MATTHAUS authored 1 year ago
  
  1553a64b
Jun 09, 2023
- IMPROVE: remove 'Chr' strings in grep commands · d60479d5
  SIRVENT MATTHAUS authored 1 year ago
  
  d60479d5
- UPDATE: typo in rules.smk - remove conda lines in commented tasks · de255dfd
  SIRVENT MATTHAUS authored 1 year ago
  
  de255dfd
- IMPROVE: add conda pragma into all rules and docler path for use with --singularity option · d2335b52
  Helene Rimbert authored 1 year ago
  
  d2335b52
- Merge branch 'helene.rimbert-master-patch-60754' into 'master' · 40c5249f
  Helene Rimbert authored 1 year ago
  
  change pattern for name of slurm outputs See merge request !4
  40c5249f
- change pattern for name of slurm outputs · d45f8128
  Helene Rimbert authored 1 year ago
  
  d45f8128
- Merge branch 'helene.rimbert-master-patch-56726' into 'master' · 15f8766f
  Helene Rimbert authored 1 year ago
  
  change partition from normal/fast to gdec on every tasks See merge request !3
  15f8766f
- change partition from normal/fast to gdec on every tasks · 964f5907
  Helene Rimbert authored 1 year ago
  
  964f5907
- IMPROVE: correction of conda env create command in README.md · 4d524bea
  Helene Rimbert authored 1 year ago
  
  4d524bea
Nov 17, 2021
- Upload New environment file for Singularity build · 4df3e943
  Helene Rimbert authored 3 years ago
  
  4df3e943
- Upload New Singularity definition file · 6da2c228
  Helene Rimbert authored 3 years ago
  
  6da2c228
Sep 08, 2021
- Update README.md · 17c71a1f
  Helene Rimbert authored 3 years ago
  
  17c71a1f
- NEW single-isoform mode for transfert between disitant varieties · bc3fc1f7
  Helene Rimbert authored 3 years ago
  
  v1.1
  
  bc3fc1f7
Aug 30, 2021
- Merge branch 'master' of https://forgemia.inra.fr/umr-gdec/magatt · 107b0ecc
  Helene Rimbert authored 3 years ago
  
  107b0ecc
- remove temp() from rules/geneAnchoring.smk rules and cumulate attributes in... · a8ed53fa
  Helene Rimbert authored 3 years ago
  
  remove temp() from rules/geneAnchoring.smk rules and cumulate attributes in final gf for prevous_id gff feaure
  a8ed53fa
May 10, 2021
- Update README.md · 355d4288
  Helene Rimbert authored 3 years ago
  
  355d4288
Apr 08, 2021
- Update environment.yml with new dependancy : pybedtools · 4b2af2ba
  Helene Rimbert authored 3 years ago
  
  4b2af2ba
Jan 18, 2021
- Merge branch 'helene.rimbert-master-patch-73205' into 'master' · 2ed95d57
  Helene Rimbert authored 4 years ago
  
  Update README.md See merge request !2
  2ed95d57
- Update README.md · ee5c615a
  Helene Rimbert authored 4 years ago
  
  ee5c615a
- Add new file e,vironment.yml to build conda environment · f21f90d5
  Helene Rimbert authored 4 years ago
  
  f21f90d5
Jan 08, 2021
- Delete README-hpc2.md · a7d50eeb
  Helene Rimbert authored 4 years ago
  
  a7d50eeb
- Delete filterBam.yaml · 7c1bb318
  Helene Rimbert authored 4 years ago
  
  7c1bb318
Dec 16, 2020
- Update README.md · 9dd5d6e3
  Helene Rimbert authored 4 years ago
  
  9dd5d6e3
Dec 15, 2020

bug: if cds and mapping attributes existed in query GFF file, values were... · 587453ca

Helene Rimbert authored 4 years ago

bug: if cds and mapping attributes existed in query GFF file, values were collapsed. Now the values correspond to the current anchring results.

587453ca