Commits · 419fd8d3b3585d0088adfa8a43a554647535d93c · igmmbioinformatics / trio-whole-exome

Nov 17, 2021
- Fixed peddy parsing script for ultra2 · 419fd8d3
  ameyner2 authored 3 years ago
  
  419fd8d3
Nov 16, 2021
- Run notes for batch 19502 · d6e57bdf
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  d6e57bdf
- First try at a CRF rapid run on ultra2 · 62f5abf3
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  62f5abf3
Oct 04, 2021
- Added final params cleanup step · 5baf6371
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  5baf6371
- Fixed relative path · dc19ab1f
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- Moved cram compression to Slurm, updated archiving SOP · 5c664b7e
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- Added a cleanup step for bcbio config and param files · c331202b
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  c331202b
- Renaming prepare bcbio config scripts for consistency · adde4a3c
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  adde4a3c
- Use short project id for log files, move to prioritization next · ca876eab
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  ca876eab
- Tidy up formatting · 5690f7f7
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- MultiQC and PED check updated to ultra2 · f7cd78e2
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- _ultra2 docs moved to main copy · 1de6ebe9
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- _ultra2 docs moved to main copy · 7fe258a1
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Sep 30, 2021
- First attempt at sbatch command for slurm system · 55e0eef2
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  55e0eef2
Sep 29, 2021
- Project id then version and date for config generation logs, copy PED file... · fd4bc70d
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  Project id then version and date for config generation logs, copy PED file rather than symbolic links
  fd4bc70d
- Fixed a few typos and clarified new output folder structure · b8b8d361
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  b8b8d361
- Using Nextera read trimming for EdGe sequencing as well as CRF - only need a... · 48222543
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  Using Nextera read trimming for EdGe sequencing as well as CRF - only need a single template & config file
  48222543
- Links rather than text copy for config files and bcbio templates · be512736
  not populated not populated authored 3 years ago
  
  be512736
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 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
- 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
- Output cleanup moved to main pipeline SOP · c59efbb0
  ameyner2 authored 3 years ago
  
  c59efbb0