Commits · 3a2520e274cf6c6521dbd3d6b70807e881650c6b · igmmbioinformatics / trio-whole-exome · GitLab

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Nov 18, 2021
- Update tool_and_data_change_tracking.md · 3a2520e2
  ameyner2 authored 3 years ago
  
  3a2520e2
- Update tool_and_data_change_tracking.md · 39a93ee5
  ameyner2 authored 3 years ago
  
  39a93ee5
- Tracks pipeline tool and data changes. · 5cdb7119
  ameyner2 authored 3 years ago
  
  5cdb7119
Nov 17, 2021
- Fix plot path · 3c4d841e
  ameyner2 authored 3 years ago
  
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- Plots for strand bias investigation · 14f39d9d
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- Initial investigation of strand bias metrics · dd4a3e4d
  ameyner2 authored 3 years ago
  
  dd4a3e4d
- Updated to include compression & md5 checksums (no archive required), and... · cf90a32a
  ameyner2 authored 3 years ago
  
  Updated to include compression & md5 checksums (no archive required), and added documentation around output file structure
  cf90a32a
- 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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- Back up on git of vcf config for VEP and G2P custom edits · 8017b98d
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- First try at a CRF rapid run on ultra2 · 62f5abf3
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Nov 02, 2021
- Removed comment · 6f301855
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- Added a comment · 88e37700
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Oct 04, 2021
- Added final params cleanup step · 5baf6371
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- README script listing and SOP order · d7807776
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- Cleaned up scripts that aren't needed on ultra2 · eb484914
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- Fixed relative path · dc19ab1f
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- Moved cram compression to Slurm, updated archiving SOP · 5c664b7e
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- Renaming and md5 checksums for all project files · 35d0594d
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- Renaming checksum files to better reflect purpose · e9bf60ba
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- First draft of Slurm params · 40862f5e
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- First draft of Slurm params · cc66bb22
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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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- Renamed to match other scripts in pipeline · f17718f1
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- Fixed Slurm directive for cpus · fde303b0
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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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Oct 02, 2021
- Slurm scheduler can handle single index job array submission · 7abf48a4
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Oct 01, 2021
- Updated to new file/folder organizational structure · 3ac08ee8
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- Make results params directory · aa6028be
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- Fixed filename/folder paths at end to match new organizational structure · 57535ba3
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Sep 30, 2021
- First attempt at sbatch command for slurm system · 55e0eef2
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- Changed to using short project id, version comes after project id, per-family... · 738e0fb5
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  Changed to using short project id, version comes after project id, per-family PED and CSV files move to results/project_version/params folder
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- Ignore unassigned reads from file_list.tsv · 08cfee1a
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- Ignore emacs save files · 9eac1d8c
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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
  fd4bc70d