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TheJacksonLaboratory
/
splicing-pipelines-nf
Repository for the Anczukow-Lab splicing pipeline
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Adds trimmomatic logs to multiqc report
#244
Vlad-Dembrovskyi
closed
3 years ago
1
Adds trimmomatic logs to report
#243
Vlad-Dembrovskyi
closed
3 years ago
0
Create a results folder with all .command.sh .command.log .command.err files for each process
#242
Vlad-Dembrovskyi
closed
2 years ago
0
Reduces ci tests
#241
Vlad-Dembrovskyi
closed
3 years ago
0
Adds singularity check in ci.yml
#240
cgpu
closed
3 years ago
1
Adds local singularity profile
#239
Vlad-Dembrovskyi
closed
3 years ago
0
Adds workdir cleanup option
#238
Vlad-Dembrovskyi
closed
3 years ago
6
Updating fasp container to be managed by non-lifebit personnel
#237
adeslatt
closed
2 years ago
0
Build Anczukow lab DockerHub repo
#236
angarb
closed
3 years ago
2
Bump Gffread tool
#235
angarb
closed
2 years ago
1
Bump Stringtie Version
#234
angarb
closed
2 years ago
1
Bump STAR version
#233
angarb
closed
2 years ago
1
Add task stat parameter to rMATS
#232
angarb
opened
3 years ago
3
Adding permission changes from master
#231
angarb
closed
3 years ago
0
SOP for STAR version bump
#230
sk-sahu
closed
2 years ago
0
SOP for rmats version bump
#229
sk-sahu
closed
2 years ago
0
Adds clipping parameter
#228
sk-sahu
closed
3 years ago
0
Running test = true on Sumner requires rmats_pairs.txt
#227
angarb
closed
2 years ago
1
Quant mode
#226
angarb
closed
3 years ago
0
Check for strandedness
#225
angarb
closed
3 years ago
0
Possible fix for folder created out of file name
#224
cgpu
closed
2 years ago
2
Collect script commands and additional pipeline run info
#223
sk-sahu
closed
3 years ago
0
Get tool versions in results directory
#222
sk-sahu
closed
3 years ago
0
Not to copy unnecessary files to results dir
#221
sk-sahu
closed
2 years ago
6
Get tool versions
#220
sk-sahu
closed
3 years ago
0
Refactor
#219
sk-sahu
closed
3 years ago
0
Collect version of all the tools in a file on results folder
#218
sk-sahu
closed
3 years ago
1
Add afterScript in the last process to remove the work/ directory
#217
cgpu
closed
2 years ago
3
Capture nextflow run command, all .command.sh commands and the tool versions
#216
cgpu
closed
3 years ago
5
Bump the rMATS tool versions
#215
sk-sahu
closed
3 years ago
2
parameterize all the google life science configs
#214
sk-sahu
closed
2 years ago
2
parameterised google.lifeSciences.bootDiskSize
#213
sk-sahu
closed
3 years ago
0
parameterise maxRetries
#212
sk-sahu
closed
3 years ago
0
parameterised max retries
#211
sk-sahu
closed
3 years ago
0
Document how much disc space is needed per sample | old: rmats tasks fail with exit 9 w/ no disk space left in the device error | Add disk in dynamic resource alloc strategy
#210
cgpu
opened
3 years ago
0
fix for samtools sort taking more memory than available
#209
sk-sahu
closed
3 years ago
1
Adds Gen3 DRS support for GETx files download
#208
sk-sahu
closed
3 years ago
2
resource modification for rmats
#207
sk-sahu
closed
3 years ago
0
Sync and merge of Lifebit copy of this repo
#206
sk-sahu
closed
3 years ago
0
CRAM files download and convertion support
#205
sk-sahu
closed
2 years ago
4
Unexpected rMATS error
#204
sk-sahu
closed
3 years ago
8
sra-tools upgrades to 2.10.8
#203
sk-sahu
closed
3 years ago
0
Change sra-tools version and its implementation
#202
sk-sahu
closed
3 years ago
3
Add stranded-ness to XS tag (refactor hardcoded logic)
#201
angarb
closed
2 years ago
4
Add clipping parameter
#200
lmurba
closed
3 years ago
1
Change outWigType to None
#199
lmurba
closed
4 years ago
0
Remove wiggle output from star
#198
lmurba
closed
4 years ago
0
Remove soft clipping
#197
lmurba
closed
4 years ago
0
Remove soft clipping
#196
lmurba
closed
4 years ago
0
human test fix
#195
lmurba
closed
4 years ago
0
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