Commits · 64e14f18247fcb2e38213367e5f429a673327bce · igmmbioinformatics / trio-whole-exome

Nov 23, 2021
- Making BCBio a param, adding Python to Conda, simplifying MD5sum checking · 64e14f18
  mwham authored 3 years ago
  
  64e14f18
- Merge branch 'mwham_develop' of... · 0a021ddb
  mwham authored 3 years ago
  
  Merge branch 'mwham_develop' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exome into mwham_develop
  0a021ddb
- Fixing fake BCBio · c1953ef5
  mwham authored 3 years ago
  
  c1953ef5
- Merge branch 'giab_test_data' into 'mwham_develop' · 0e45c32f
  mwham authored 3 years ago
  
  Giab test data See merge request !2
  0e45c32f
Nov 15, 2021
- Adding BCBio config, connecting up workflows properly · ab4f1f5d
  mwham authored 3 years ago
  
  ab4f1f5d
- GIAB test data script downloads & extracts small sets of reads for 3 trios · 2f6dc35d
  not populated not populated authored 3 years ago
  
  2f6dc35d
Oct 14, 2021
- Making file checking its own script · 3dc7bc2f
  mwham authored 3 years ago
  
  3dc7bc2f
Oct 08, 2021
- Running NextFlow with -bg · d8d87bf9
  mwham authored 3 years ago
  
  d8d87bf9
- Initial commit of process for fetching Genome in a Bottle test data · af6a1054
  not populated not populated authored 3 years ago
  
  af6a1054
Oct 06, 2021
- Trying local conda env for build · c4eb6a42
  mwham authored 3 years ago
  
  c4eb6a42
- Trying local conda env for build · d8b467bc
  mwham authored 3 years ago
  
  d8b467bc
Oct 05, 2021
- Adding gitlab-ci.yml · 09fb1118
  mwham authored 3 years ago
  
  09fb1118
- Initial commit of NextFlow pipeline - test data and MD5 checks · 2ca0e60c
  mwham authored 3 years ago
  
  2ca0e60c
Sep 07, 2021
- 19258 run notes · 06de3480
  ameyner2 authored 3 years ago
  
  06de3480
Aug 30, 2021
- Fix numbering · bdbf8ed2
  ameyner2 authored 3 years ago
  
  bdbf8ed2
- Initial draft of ultra2 SOP · 6fa150fb
  ameyner2 authored 3 years ago
  
  6fa150fb
- Ultra2 version of alignment & variant calling SOP · cb00f26e
  ameyner2 authored 3 years ago
  
  cb00f26e
Aug 26, 2021
- 19188 run notes first draft · d6b7860e
  ameyner2 authored 3 years ago
  
  d6b7860e
Aug 23, 2021
- Fixed resource path · 02451088
  not populated not populated authored 3 years ago
  
  02451088
- Fixed a couple of resource paths · 15f1e1b2
  ameyner2 authored 3 years ago
  
  15f1e1b2
- Removed gnomad genomes from bcbio software installation. · f0535475
  ameyner2 authored 3 years ago
  
  f0535475
- Updated file paths to ultra2 & reorganized resources folder · dfe274bf
  not populated not populated authored 3 years ago
  
  dfe274bf
- Added emacs · ba46f842
  ameyner2 authored 3 years ago
  
  ba46f842
- Fixed formatting for bulleted list · b05a6512
  ameyner2 authored 3 years ago
  
  b05a6512
- Updated to reflect more structured organization of resources folder, and new... · 78b0477d
  ameyner2 authored 3 years ago
  
  Updated to reflect more structured organization of resources folder, and new versions of gnomAD exomes (r2.1.1) and genomes (r3.1.1)
  78b0477d
- Update Resources_ultra2.md · 283fc0ca
  ameyner2 authored 3 years ago
  
  283fc0ca
Aug 18, 2021
- Start of resources documentation for ultra2 · 31ea8706
  ameyner2 authored 3 years ago
  
  31ea8706
- Fixed file paths · 1532172e
  ameyner2 authored 3 years ago
  
  1532172e
- Update Software_installation_ultra2.md · 467d20c4
  ameyner2 authored 3 years ago
  
  467d20c4
- Skipping dev tools upgrade - fixed in v1.2.8 bcbio · 4e1a5a34
  ameyner2 authored 3 years ago
  
  4e1a5a34
Aug 13, 2021
- Update Software_installation_ultra2.md · ba17b78c
  ameyner2 authored 3 years ago
  
  ba17b78c
- Fix project > u035/shared. · 43b11fd0
  ameyner2 authored 3 years ago
  
  43b11fd0
- Initial commit of variant prioritization set up. · 01affb5e
  ameyner2 authored 3 years ago
  
  01affb5e
- Update Software_installation_ultra2.md · d667bfff
  ameyner2 authored 3 years ago
  
  d667bfff
- Initial documentation of software installation on ultra2 (sdf-cs1) at... · 537f6c09
  ameyner2 authored 3 years ago
  
  Initial documentation of software installation on ultra2 (sdf-cs1) at EIDF/EPCC. Got as far as executing bcbio base installation.
  537f6c09
Jul 21, 2021
- Moved output cleanup to main pipeline doc · 06a48fb1
  ameyner2 authored 3 years ago
  
  ultra_last_commit
  
  06a48fb1
- Updates to prioritization scripts · 41e4ff2a
  ameyner2 authored 3 years ago
  
  41e4ff2a
- Output cleanup moved to main pipeline SOP · c59efbb0
  ameyner2 authored 3 years ago
  
  c59efbb0
Jul 14, 2021
- Update 18610_run_notes.md · 17704038
  ameyner2 authored 3 years ago
  
  17704038
- Fixed name · e4b56827
  ameyner2 authored 3 years ago
  
  e4b56827