UCSF-Costello-Lab LG3_Pipeline issues

UCSF-Costello-Lab / 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PERFORMANCE: ANNOVAR says index file is out of date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 2 years ago
1
NEWS: Update for important changes

#156 HenrikBengtsson opened 2 years ago
0
scripts/Align_mem.sh: Why was `${SAMTOOLS} index ...` dropped?

#155 HenrikBengtsson opened 2 years ago
2
assert_pwd: It's there for a reason

#154 HenrikBengtsson closed 2 years ago
2
develop_c4: Add back `# shellcheck source=scripts/utils.sh`

#153 HenrikBengtsson opened 2 years ago
2
make check errors on develop_c4 branch

#152 HenrikBengtsson opened 2 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 2 years ago
2
bin/lg3-status: ShellCheck issues

#150 HenrikBengtsson opened 2 years ago
5
runs_demo/{_run_PSCN,_run_PSCN1-5}: ShellCheck issues

#149 HenrikBengtsson closed 2 years ago
1
facets.pbs: ShellCheck issues

#148 HenrikBengtsson closed 2 years ago
1
CI: Migrate to GitHub Actions

#147 HenrikBengtsson closed 2 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 2 years ago
2
CLEANUP: Use same JAVA everywhere

#138 HenrikBengtsson closed 2 years ago
2
CLEANUP: Set PYTHON to stable python version and use everywhere

#137 HenrikBengtsson closed 2 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 4 years ago
2
DESIGN: Pipeline and project settings (lg3.conf, env vars, ...)

#130 HenrikBengtsson closed 4 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 4 years ago
11
lg3.conf: Incorporate in all scripts

#127 HenrikBengtsson closed 4 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