Commits · master · amunoz / structuralvariants_poc

30 Jun, 2022 2 commits
- Removed scripts from inputs and updated templates · a5daaac5
  amunoz authored Jun 30, 2022
  
  a5daaac5
- Removed gridss_filter and collapse scripts from input · 2a9af241
  amunoz authored Jun 30, 2022
  
  2a9af241
27 Jun, 2022 1 commit
- Updated merge_all script and final_filtering subworkflow · b21e4d3d
  amunoz authored Jun 27, 2022
  
  b21e4d3d
23 Jun, 2022 7 commits
- Merge branch 'master' of https://gitlab.bsc.es/amunoz/structuralvariants_poc · 9647b0bf
  lrodrin authored Jun 23, 2022
  
  9647b0bf
- minor changes in main.nf and modules/gridss.nf · e79224f4
  amunoz authored Jun 23, 2022
  
  e79224f4
- Param added to nextflow.config · 248c89aa
  amunoz authored Jun 23, 2022
  
  248c89aa
- Params added to cnv_gridss · ff2fff6a
  amunoz authored Jun 23, 2022
  
  ff2fff6a
- Param added to cnv_gridss · e6f71ceb
  Adrián Muñoz authored Jun 23, 2022
  
  e6f71ceb
- Merge branch 'master' of https://gitlab.bsc.es/amunoz/structuralvariants_poc · 9f6f3a6f
  amunoz authored Jun 23, 2022
  
  9f6f3a6f
- Merge branch 'master' of https://gitlab.bsc.es/lrodrig1/structuralvariants_poc · b3f96121
  amunoz authored Jun 23, 2022
  
  b3f96121
22 Jun, 2022 9 commits
- remove test inputs for modules/manta.nf · b87577af
  lrodrig1 authored Jun 22, 2022
  
  b87577af
- passing params from main to modules in manta subworkflow · 0ee8e6c6
  lrodrig1 authored Jun 22, 2022
  
  0ee8e6c6
- add publishDir in modules/collapse.nf · bbfbc553
  lrodrig1 authored Jun 22, 2022
  
  bbfbc553
- add split basename in modules/bedops_union.nf · a4a4ca68
  lrodrig1 authored Jun 22, 2022
  
  a4a4ca68
- minor changes in modules/svtools.nf · 69691bbc
  lrodrig1 authored Jun 22, 2022
  
  69691bbc
- gridss updated · aef7ba2b
  Acivico authored Jun 22, 2022
  
  aef7ba2b
- update manta.nf · ebd95323
  lrodrig1 authored Jun 22, 2022
  
  ebd95323
- gunzip added · 29cdf23e
  Acivico authored Jun 22, 2022
  
  29cdf23e
- Add gunzip to bwa_index · 715c514b
  Acivico authored Jun 22, 2022
  
  715c514b
21 Jun, 2022 1 commit
- Manta, svtools and manta_filter fix · d349f9ae
  amunoz authored Jun 21, 2022
  
  d349f9ae
20 Jun, 2022 3 commits
- Update manta · 7ffd0851
  Acivico authored Jun 20, 2022
  
  7ffd0851
- Minor changes in the cnv's · 0ae880d7
  Acivico authored Jun 20, 2022
  
  0ae880d7
- Merge branch 'master' of https://gitlab.bsc.es/lrodrig1/structuralvariants_poc · 08ca4872
  Acivico authored Jun 20, 2022
  
  08ca4872
17 Jun, 2022 2 commits
- add publishDir on bam filtering subworkflow in Nextflow · 0f0fc8d7
  lrodrig1 authored Jun 17, 2022
  
  0f0fc8d7
- minor changes to bam filtering in Nextflow · 2f365102
  lrodrig1 authored Jun 17, 2022
  
  2f365102
16 Jun, 2022 6 commits
- minor changes in picard markduplicates in Nextflow · dfb2162d
  lrodrig1 authored Jun 16, 2022
  
  dfb2162d
- Updated bwa_index · 5cdd0e69
  amunoz authored Jun 16, 2022
  
  5cdd0e69
- Merge · 5abaf10d
  amunoz authored Jun 16, 2022
  
  5abaf10d
- update nextflow.config with 5 samples · c455a945
  lrodrig1 authored Jun 16, 2022
  
  c455a945
- remove samtools index+merge subworkflows in Nextflow · 3d7f911f
  lrodrig1 authored Jun 16, 2022
  
  3d7f911f
- minor changes on bwa mem and samtools view+sort of Nextflow modules · ad399cc9
  lrodrig1 authored Jun 16, 2022
  
  ad399cc9
15 Jun, 2022 4 commits
- minor changes in samtools_sort.nf · cfc8d12a
  lrodrig1 authored Jun 15, 2022
  
  cfc8d12a
- minor changes in samtools_view_sam2bam.nf · 6524520c
  lrodrig1 authored Jun 15, 2022
  
  6524520c
- read_group as optional parameter · 3d20b78c
  amunoz authored Jun 15, 2022
  
  3d20b78c
- add Daniel as an author in nextflow.config · 8d50ef42
  lrodrig1 authored Jun 15, 2022
  
  8d50ef42
14 Jun, 2022 5 commits
- add list of reference index fasta files in nextflow.config · b6deadc0
  lrodrig1 authored Jun 14, 2022
  
  b6deadc0
- remove BUNDLE FILES include and add conditional index files generation in main.nf · 786fad21
  lrodrig1 authored Jun 14, 2022
  
  786fad21
- divide reads and indexFiles of bwa-mem modules and subworkflow · d727a3d7
  lrodrig1 authored Jun 14, 2022
  
  d727a3d7
- added emit to ouput of bwa_index.nf · 05efb875
  lrodrig1 authored Jun 14, 2022
  
  05efb875
- change order of steps and add two outputs in bwa_index.nf subworkflow · fb76c9c7
  lrodrig1 authored Jun 14, 2022
  
  fb76c9c7