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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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Make Java respect TMPDIR
#172
HenrikBengtsson
opened
2 years ago
0
Passing parameters to qsub
#171
ivan108
opened
2 years ago
1
Add built-in support for `lg3 run QC1`, `lg3 run QC2`, and `lg3 run QC3`
#170
HenrikBengtsson
opened
2 years ago
3
LG3 add-on examples assume write permission to ${LG3_HOME}
#169
HenrikBengtsson
opened
2 years ago
0
REPRODUCIBILITY: lg3 2021-10-11
#168
HenrikBengtsson
opened
2 years ago
0
lg3 run PostMut: Does not respect ./lg3.conf
#167
HenrikBengtsson
closed
2 years ago
2
Add assert_java_1.6() to assert Java is of version 1.6.x
#166
HenrikBengtsson
opened
2 years ago
0
lg3 run Recall: Rscript sources user's ~/.Rprofile, if it exists
#165
HenrikBengtsson
closed
2 years ago
1
lg3 run <step>
#164
HenrikBengtsson
closed
2 years ago
1
C4: qsub wrapper does not support CLI option `-d <path>`
#163
HenrikBengtsson
closed
2 years ago
1
RELEASE: lg3 2021-10-08
#162
HenrikBengtsson
closed
2 years ago
3
REPRODUCIBILITY: Comparing lg3 2021-10-08 to previous version 2020-05-16
#161
HenrikBengtsson
opened
2 years ago
0
WARN: undefined variables MQRankSum and ReadPosRankSum
#160
HenrikBengtsson
opened
2 years ago
2
PERFORMANCE: ANNOVAR says index file is out of date
#159
HenrikBengtsson
opened
2 years ago
0
RESOURCES: Resource files used
#158
HenrikBengtsson
opened
2 years ago
3
Make it possible to override the default software paths
#157
HenrikBengtsson
closed
3 years ago
1
NEWS: Update for important changes
#156
HenrikBengtsson
opened
3 years ago
0
scripts/Align_mem.sh: Why was `${SAMTOOLS} index ...` dropped?
#155
HenrikBengtsson
opened
3 years ago
2
assert_pwd: It's there for a reason
#154
HenrikBengtsson
closed
3 years ago
2
develop_c4: Add back `# shellcheck source=scripts/utils.sh`
#153
HenrikBengtsson
opened
3 years ago
2
make check errors on develop_c4 branch
#152
HenrikBengtsson
opened
3 years ago
7
muTect: Try to switch from muTect-1.0.27783 to a newer version, e.g. muTect-1.1.1 or muTect-1.1.4
#151
HenrikBengtsson
opened
3 years ago
2
bin/lg3-status: ShellCheck issues
#150
HenrikBengtsson
opened
3 years ago
5
runs_demo/{_run_PSCN,_run_PSCN1-5}: ShellCheck issues
#149
HenrikBengtsson
closed
3 years ago
1
facets.pbs: ShellCheck issues
#148
HenrikBengtsson
closed
3 years ago
1
CI: Migrate to GitHub Actions
#147
HenrikBengtsson
closed
3 years ago
2
SOFTWARE: Identify software tools for TIPCC-to-C4 migration
#146
HenrikBengtsson
closed
2 years ago
16
lg3 test validate: Compare content of FASTQ and BWA BAM files
#145
HenrikBengtsson
closed
4 years ago
3
REPRODUCIBILITY: Comparing lg3 2020-05-16 to previous versions
#144
HenrikBengtsson
opened
4 years ago
0
REPRODUCIBILITY: Comparing lg3 2019-07-22 to previous versions
#143
HenrikBengtsson
opened
4 years ago
1
REPRODUCIBILITY: Comparing lg3 2019-03-23 to previous versions
#142
HenrikBengtsson
opened
4 years ago
1
REPRODUCIBILITY: Comparing lg3 2018-12-27 to previous versions
#141
HenrikBengtsson
opened
4 years ago
2
TESTS: Unit testing `lg3 test validate`
#140
HenrikBengtsson
opened
4 years ago
0
CLEANUP: Use same SAMTOOLS everywhere
#139
HenrikBengtsson
closed
3 years ago
2
CLEANUP: Use same JAVA everywhere
#138
HenrikBengtsson
closed
3 years ago
2
CLEANUP: Set PYTHON to stable python version and use everywhere
#137
HenrikBengtsson
closed
3 years ago
1
ROBUSTNESS: Validate Python version
#136
HenrikBengtsson
closed
4 years ago
1
Error in "./_run_Pindel"
#135
t-nejo
closed
4 years ago
9
ROBUSTNESS: Use ${LG3_HOME:?} instead of ${LG3_HOME?} since it also err on empty values
#134
HenrikBengtsson
closed
4 years ago
1
feature/lg3.conf: Not in sync with master branch
#133
HenrikBengtsson
opened
4 years ago
13
feature/lg3.conf: check errors
#132
HenrikBengtsson
closed
2 years ago
1
ROBUSTNESS: `./lg3.conf` must not be edited while running pipeline
#131
HenrikBengtsson
opened
5 years ago
2
DESIGN: Pipeline and project settings (lg3.conf, env vars, ...)
#130
HenrikBengtsson
closed
5 years ago
2
ROBUSTNESS: Protect against running the pipeline from within the LG3_HOME folder
#129
HenrikBengtsson
closed
5 years ago
1
BREAKING/BUG: $LG3_HOME/lg3.conf prevents env vars to be set in run scripts
#128
HenrikBengtsson
closed
5 years ago
11
lg3.conf: Incorporate in all scripts
#127
HenrikBengtsson
closed
5 years ago
2
PROPOSAL: Create empty ./lg3.conf, iff missing?
#126
HenrikBengtsson
opened
5 years ago
3
BUG(?): R_LIBS_USER=~/R/%p-library/%v /opt/R/R-latest/bin/Rscript: No such file or directory
#125
HenrikBengtsson
closed
5 years ago
4
ShellCheck error in scripts/Mutect2_TvsN.sh
#124
HenrikBengtsson
closed
5 years ago
2
Next release: 2019-03-23
#123
HenrikBengtsson
closed
5 years ago
7
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