Commits · 5c664b7ecfd535014d8422ceb5ce3cc3f3d486cb · igmmbioinformatics / trio-whole-exome

Oct 04, 2021
- 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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- Renaming prepare bcbio config scripts for consistency · adde4a3c
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- Use short project id for log files, move to prioritization next · ca876eab
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- 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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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
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- Fixed a few typos and clarified new output folder structure · b8b8d361
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- 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
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- Links rather than text copy for config files and bcbio templates · be512736
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Sep 07, 2021
- 19258 run notes · 06de3480
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Aug 30, 2021
- Fix numbering · bdbf8ed2
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- Initial draft of ultra2 SOP · 6fa150fb
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- Ultra2 version of alignment & variant calling SOP · cb00f26e
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Aug 26, 2021
- 19188 run notes first draft · d6b7860e
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Aug 23, 2021
- Fixed a couple of resource paths · 15f1e1b2
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- Removed gnomad genomes from bcbio software installation. · f0535475
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- Added emacs · ba46f842
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- Fixed formatting for bulleted list · b05a6512
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- 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)
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- Update Resources_ultra2.md · 283fc0ca
  ameyner2 authored 3 years ago
  
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Aug 18, 2021
- Start of resources documentation for ultra2 · 31ea8706
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- Fixed file paths · 1532172e
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- Update Software_installation_ultra2.md · 467d20c4
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- Skipping dev tools upgrade - fixed in v1.2.8 bcbio · 4e1a5a34
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Aug 13, 2021
- Update Software_installation_ultra2.md · ba17b78c
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- Fix project > u035/shared. · 43b11fd0
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- Initial commit of variant prioritization set up. · 01affb5e
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- Update Software_installation_ultra2.md · d667bfff
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- 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.
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Jul 21, 2021
- Moved output cleanup to main pipeline doc · 06a48fb1
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- Output cleanup moved to main pipeline SOP · c59efbb0
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Jul 14, 2021
- Update 18610_run_notes.md · 17704038
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- Fixed name · e4b56827
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- Update 18170_run_notes.md · 040a60c6
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- Update 17200_ITPR1_mosaic_investigation.md · 14f25b8c
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- Add new file · 299d4475
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