Commits · 44dc72972f4722ecfacce153a4513f881e598db1 · UMR GDEC / magatt

Jun 16, 2020
- force python to execute version 3.5 · 44dc7297
  Helene Rimbert authored 4 years ago
  
  44dc7297
May 29, 2020
- all gmap anchoring integrated into the final HC and LC gff instead of a third _rescue.gff3 file · e51b6a52
  Helene Rimbert authored 4 years ago
  
  e51b6a52
- new rules to validate cds using fastavalidecds from Exonerate package · 0bee6560
  Helene Rimbert authored 4 years ago
  
  0bee6560
May 28, 2020
- 1st dev fial version · 08268dae
  Helene Rimbert authored 4 years ago
  
  v0.1
  
  08268dae
May 14, 2020
- convertion of the gff file from GMAP after the rescue of misaligned genes is OK. · d0910f29
  Helene Rimbert authored 4 years ago
  
  d0910f29
- ISBPs are now allowed to have some mismatches in the alignment. parameters... · 00d0109a
  Helene Rimbert authored 4 years ago
  
  ISBPs are now allowed to have some mismatches in the alignment. parameters have been added into the config.yaml file and are used accordingly in the rules and filterBam.py script
  00d0109a
May 06, 2020
- new rule gmapIndexTarget to prepare the whole genome index of the target... · 7ded6fa6
  Helene Rimbert authored 4 years ago
  
  new rule gmapIndexTarget to prepare the whole genome index of the target genome. This index is needed to rescue genes without any mapping result in targeted mapping and gmap on target
  7ded6fa6
- add chromosome name in message of rulegmapRescue · 31eb2bd0
  Helene Rimbert authored 4 years ago
  
  31eb2bd0
May 04, 2020
- BUG: remove option -w in fgrep which causes grep of genes from Unknown chromosome to fail · 34abf1a4
  Helene Rimbert authored 4 years ago
  
  34abf1a4
- BUG: new rule to deal with genes without valid pair of markers · 168392a6
  Helene Rimbert authored 4 years ago
  
  168392a6
- BUG: remove -w from the fgrep command in the split per chrom rule. This cause... · ee0ee67d
  Helene Rimbert authored 4 years ago
  
  BUG: remove -w from the fgrep command in the split per chrom rule. This cause a bug resulting into empty output
  ee0ee67d
Feb 10, 2020
- new rule splitISBP:task is now parallelised per chromosome · 6132a27f
  Helene Rimbert authored 5 years ago
  
  6132a27f
- bug in mapHomologousRegions shell command: need to use {wildcards.chrom}... · 55131a1a
  Helene Rimbert authored 5 years ago
  
  bug in mapHomologousRegions shell command: need to use {wildcards.chrom} instead of {chrom} in the shell to properly expand the chrom variable
  55131a1a
Feb 07, 2020
- parallel upstream and downstream marker per chromosome · ea50b37d
  Helene Rimbert authored 5 years ago
  
  ea50b37d
Jan 17, 2020
- Final version of blatMapping pipeline · 13be85a0
  Helene Rimbert authored 5 years ago
  
  13be85a0
Dec 20, 2019
- add result directory to gitignore file, remove markersIds from mapping pipeline · 7465d454
  Helene Rimbert authored 5 years ago
  
  7465d454
Dec 17, 2019
- new snakemake rule geneAnchoring.smk · 16d31b3b
  Helene Rimbert authored 5 years ago
  
  16d31b3b
Dec 16, 2019
- add indexing of reference sequences with samtools faidx · 479d76b6
  Helene Rimbert authored 5 years ago
  
  479d76b6
- update snakemake rules · 953851b9
  Helene Rimbert authored 5 years ago
  
  953851b9
- revert from nextflow to snakemake · 5b5d9130
  Helene Rimbert authored 5 years ago
  
  5b5d9130
Sep 16, 2019
- new config cluster.json for slurm compatibility · cf4d67c7
  Helene Rimbert authored 5 years ago
  
  cf4d67c7
Jul 10, 2019
- reformat gmap.smk · 674db69b
  Helene Rimbert authored 5 years ago
  
  674db69b
Jul 05, 2019
- BUG: output directory not detected by snakemake. needed to add directory()... · 32047fe2
  Helene Rimbert authored 5 years ago
  
  BUG: output directory not detected by snakemake. needed to add directory() statement for the gmapstats output.
  32047fe2
- add gmap.smk rules · 9f3e8b06
  Helene Rimbert authored 5 years ago
  
  9f3e8b06

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