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UCSF-Costello-Lab
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LG3_Pipeline
The original LG3 pipeline
https://github.com/UCSF-Costello-Lab/LG3_Pipeline
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WISH: Add support for latest Pindel
#122
shuntsman-ucsf
closed
5 years ago
41
Next release: 2018-12-27
#121
HenrikBengtsson
closed
5 years ago
1
TESTS: Test data set for _run_Recal_pass2
#120
HenrikBengtsson
opened
5 years ago
0
Error in Recal_pass2 after QC and making symlinks
#119
shuntsman-ucsf
closed
5 years ago
14
ERRORS: make check errors
#118
HenrikBengtsson
closed
5 years ago
2
Next release: 2018-12-20
#117
HenrikBengtsson
closed
5 years ago
4
WISH: Is there an existing identity check for tumor/normal samples?
#116
shuntsman-ucsf
closed
5 years ago
1
WISH: Add (optional) support for MuTect2
#115
HenrikBengtsson
opened
5 years ago
4
Recal_pass2 not completing for Patients with merged Normal files
#114
shuntsman-ucsf
closed
5 years ago
4
Next release: 2018-11-12
#113
HenrikBengtsson
closed
5 years ago
7
ERROR: Recal.pbs is gone
#112
HenrikBengtsson
closed
5 years ago
1
assertion functions - debug output (also when everything is OK)
#111
ivan108
opened
5 years ago
6
Unused code?
#110
ivan108
closed
5 years ago
3
TESTS: Add unit tests, e.g. test a specific step
#109
HenrikBengtsson
opened
5 years ago
0
Check errors
#108
HenrikBengtsson
closed
5 years ago
5
CLEANUP: Rename some `PICARD` to `PICARD_HOME`
#107
HenrikBengtsson
closed
5 years ago
5
WISH: Have errors report on script and line number
#106
HenrikBengtsson
closed
5 years ago
7
Utility functions: file and directory assertions
#105
HenrikBengtsson
closed
5 years ago
2
Next release
#104
HenrikBengtsson
closed
5 years ago
2
BUG: scratch disk directories are not completely removed after job is done
#103
ivan108
closed
5 years ago
22
REQUEST: _run_PostMut (chk_mutdet.sh) should allow alternate patient_id_conversions.tsv files
#102
shuntsman-ucsf
closed
5 years ago
1
CRLF line ending: support them or give an error?
#101
HenrikBengtsson
closed
5 years ago
2
ROBUSTNESS: Validate correctness of TSV file content
#100
HenrikBengtsson
opened
5 years ago
1
ROBUSTNESS: Add more run-time assertion of variables
#99
HenrikBengtsson
closed
5 years ago
1
Error when running MutDet "invalid -v syntax"
#98
shuntsman-ucsf
closed
5 years ago
15
CHECK ERROR: Invalid path in develop branch
#97
HenrikBengtsson
closed
5 years ago
5
CODE STYLE: Define error() function to replace echo "..." | exit 1
#96
HenrikBengtsson
closed
5 years ago
3
CODE STYLE: Use more informative env var names than e.g. PYTHON_SCRIPT_A
#95
HenrikBengtsson
closed
5 years ago
9
Occasional Failures during Align_fastq.sh
#94
shuntsman-ucsf
opened
5 years ago
1
How should we handle Patients with multiple Normal samples?
#93
shuntsman-ucsf
opened
5 years ago
7
Possible Error running Merge
#92
shuntsman-ucsf
closed
5 years ago
15
WISH: skip steps in Recal
#91
ivan108
opened
5 years ago
6
Next release
#90
HenrikBengtsson
closed
5 years ago
2
ROBUSTNESS: Remove default LG3_HOME value - give error instead
#89
HenrikBengtsson
closed
5 years ago
1
TODO: integrate exomeQualityPlots scripts into LG3 pipeline
#88
ivan108
opened
5 years ago
10
Remove `bigmem` resource request from PBS script
#87
HenrikBengtsson
closed
5 years ago
9
Updating NEWS
#86
HenrikBengtsson
closed
5 years ago
1
Check errors
#85
HenrikBengtsson
closed
5 years ago
3
NEW API: lg3 ... commands for running pipeline
#84
HenrikBengtsson
closed
2 years ago
3
CLEANUP: Delete some *.pbs or scripts/* files?
#83
HenrikBengtsson
closed
5 years ago
6
HOW TO: Overriding default qsub PBS directives (e.g. memory and core resource settings)
#82
HenrikBengtsson
closed
5 years ago
1
BUG: Pindel doesn't support underscores in PATIENT
#81
HenrikBengtsson
closed
5 years ago
3
Request info for fields in 'patient_ID_conversions.tsv'
#80
shuntsman-ucsf
opened
5 years ago
6
Add support for additional underscores and more in FASTQ file names
#79
HenrikBengtsson
closed
5 years ago
1
Error towards end of TRIM on batch run
#78
shuntsman-ucsf
closed
5 years ago
23
ROBUSTNESS: Relay errors in more places
#77
HenrikBengtsson
closed
5 years ago
3
Module lg3/devel broken??
#76
ivan108
closed
5 years ago
3
HOW TO: Set up a personal `module load lg3/devel`
#75
HenrikBengtsson
closed
5 years ago
2
Deprecated LG3_INPUT_ROOT and LG3_OUTPUT_ROOT
#74
HenrikBengtsson
opened
5 years ago
4
Initial setup with new release
#73
ivan108
closed
5 years ago
15
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