Commits · eb484914740b3412067f02c10eeb758b5ab550d2 · igmmbioinformatics / trio-whole-exome · GitLab

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Oct 04, 2021
- 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
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- Fixed output folder path · ece87972
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- Fixed output folder path · 9c9d1746
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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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- Corrected and simplified file paths for ultra2 · 5262d001
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- Merge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exome · c418de42
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- Santosh-specific PED file manipulation · 57ec650c
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Sep 07, 2021
- 19258 run notes · 06de3480
  ameyner2 authored 3 years ago
  
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Aug 30, 2021
- Fix numbering · bdbf8ed2
  ameyner2 authored 3 years ago
  
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- Initial draft of ultra2 SOP · 6fa150fb
  ameyner2 authored 3 years ago
  
  6fa150fb
- Ultra2 version of alignment & variant calling SOP · cb00f26e
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Aug 26, 2021
- 19188 run notes first draft · d6b7860e
  ameyner2 authored 3 years ago
  
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Aug 23, 2021
- Fixed resource path · 02451088
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- Fixed a couple of resource paths · 15f1e1b2
  ameyner2 authored 3 years ago
  
  15f1e1b2