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TheJacksonLaboratory
/
splicing-pipelines-nf
Repository for the Anczukow-Lab splicing pipeline
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CloudOS optimisation
#194
sk-sahu
closed
4 years ago
0
fix star_index bug
#193
lmurba
closed
4 years ago
1
Fix bug with star_index when only running the second half of the pipeline
#192
lmurba
closed
4 years ago
0
mega_time added to config
#191
angarb
closed
4 years ago
2
star_overhangs/star_${params.readlength}' is bug prone, as the user can define any readlength
#190
cgpu
closed
4 years ago
1
Optimise resources utilised (memory, disk space)
#189
sk-sahu
closed
4 years ago
2
Identify processes with memory errors and update errorStrategy to allow retry with increased memory
#188
cgpu
closed
4 years ago
7
Changes from dynamic memory to fixed 30GB in get_accession
#187
sk-sahu
closed
4 years ago
0
Update memory for get_accession
#186
lmurba
closed
4 years ago
0
Not enough RAM for SRA get_accession
#185
lmurba
closed
4 years ago
0
STAR improvements
#184
sk-sahu
closed
4 years ago
7
Failed to publish file: java.io.IOException: No space left on device #3
#183
cgpu
closed
4 years ago
3
Solves rMATS uneven input
#182
sk-sahu
closed
4 years ago
0
Update path to star index
#181
lmurba
closed
4 years ago
10
Fixed singleEnd check for TCGA bams
#180
PhilPalmer
closed
4 years ago
1
minor fixes with rmats_out channel
#179
sk-sahu
closed
4 years ago
0
Fixes rmats output copy
#178
sk-sahu
closed
4 years ago
1
Improve rmats config
#177
sk-sahu
closed
4 years ago
0
Get output file with all `command.sh` scripts
#176
lmurba
closed
3 years ago
6
Human Test Is Not Working
#175
angarb
closed
4 years ago
0
add keepbothreads variable to Trimmomatic
#174
angarb
closed
4 years ago
1
Create a 'big job' option in STAR
#173
angarb
closed
4 years ago
9
Adds a new param star_memory
#172
sk-sahu
closed
4 years ago
0
Modification on error handling
#171
sk-sahu
closed
4 years ago
0
Unequal B1 and B2
#170
angarb
closed
4 years ago
0
increases disk space for master node and STAR process
#169
sk-sahu
closed
4 years ago
0
Increased disk from 100GB -> 2TB on google master node
#168
PhilPalmer
closed
4 years ago
0
Changed error strategy, increased star disk and resources
#167
PhilPalmer
closed
4 years ago
0
Fix test run
#166
lmurba
closed
4 years ago
0
add `IncFormLen` and `SkipFormLen` to output file
#165
lmurba
closed
4 years ago
0
Keep Inc and SkipFormLen in post processing
#164
lmurba
closed
4 years ago
0
Added check_max funcion to google config
#163
PhilPalmer
closed
4 years ago
0
Updated google resources
#162
PhilPalmer
closed
4 years ago
0
update trimmomatic parameters
#161
lmurba
closed
4 years ago
0
Changing Trimmomatic parameter #5, minAdapterLength
#160
angarb
closed
4 years ago
0
Increased star resources for gcloud
#159
PhilPalmer
closed
4 years ago
0
Change Trimmomatic parameters for SE reads
#158
angarb
closed
4 years ago
1
Adding hg19 to 'assembly_name' parameter options and post processing
#157
angarb
opened
4 years ago
1
BigWig Folder
#156
angarb
closed
4 years ago
1
Updated google star memory
#155
PhilPalmer
closed
4 years ago
0
Fixed check for paired BAM and decreased google resources again
#154
PhilPalmer
closed
4 years ago
0
Revert "Decreased/optimised resources for GCloud"
#153
PhilPalmer
closed
4 years ago
0
Decreased/optimised resources for GCloud
#152
PhilPalmer
closed
4 years ago
0
Added check for paired vs single-end BAMs from TCGA
#151
PhilPalmer
closed
4 years ago
0
When STAR index is pulled based on 'readlength' parameter, it currently pulls human (not mouse).
#150
angarb
closed
4 years ago
3
Update sumner resources as per #146
#149
PhilPalmer
closed
4 years ago
0
update sjdb overhang
#148
lmurba
closed
4 years ago
0
fix postprocessing bug
#147
lmurba
closed
4 years ago
0
Improve the requested resources on Sumner
#146
PhilPalmer
closed
4 years ago
3
Update run_on_sumner.md
#145
angarb
closed
4 years ago
0
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