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mskcc
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pluto-cwl
CWL workflows for helix filter scripts
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remove task failure suppression
#72
stevekm
closed
2 years ago
1
Need input & output of related samples for reporting
#71
stevekm
closed
2 years ago
1
incorporate dos2unix into samples fillout workflow (resurrection workflow)
#70
stevekm
opened
3 years ago
1
update workflow.cwl to include more recent pipeline outputs and refactors
#69
stevekm
opened
3 years ago
0
new facets suite container is breaking the workflow
#68
stevekm
closed
2 years ago
5
test in pluto
#67
allanbolipata
closed
3 years ago
0
portal/data_clinical_sample.txt file is missing pipeline version
#66
timosong
opened
3 years ago
3
Portal files output needs new line (meta_mutations_extended.txt)
#65
timosong
closed
3 years ago
2
Incorporate DMP copy number information (resurrection)
#64
timosong
closed
3 years ago
1
Make data_mutations_uncalled and meta_mutations_uncalled files for cBioPortal
#63
stevekm
opened
3 years ago
2
add "print json" method to run script
#62
stevekm
closed
2 years ago
2
refactor samples fillout methods
#61
stevekm
closed
3 years ago
1
add OncoKB annotation to maf output
#60
stevekm
opened
3 years ago
0
Dev
#59
allanbolipata
closed
3 years ago
0
Fix/update mem
#58
allanbolipata
closed
3 years ago
0
Need to get a run metadata samplesheet
#57
stevekm
closed
2 years ago
1
update_cBioPortal_data.py merge_mafs uses too much memory
#56
stevekm
closed
3 years ago
3
documentation for developers
#55
stevekm
closed
2 years ago
2
switch to a testing framework that supports parallel execution
#54
stevekm
closed
2 years ago
4
pipeline tools documentation for PI's
#53
stevekm
opened
3 years ago
1
add sample concordance / discordance comparisons
#52
stevekm
opened
3 years ago
0
need to scrub sample IDs from demo dataset
#51
stevekm
closed
2 years ago
2
create mini test bam files, standardized mini test maf files
#50
stevekm
closed
3 years ago
2
Add MSI to the workflow
#49
stevekm
closed
3 years ago
1
IGV reports sort by base
#48
stevekm
closed
3 years ago
1
Add sample vs. cohort plots to reporting
#47
stevekm
opened
3 years ago
0
Need pipeline reports
#46
stevekm
closed
3 years ago
4
use .bed file for IGV report sites
#45
stevekm
opened
3 years ago
1
add more columns to cBio utils module
#44
stevekm
closed
3 years ago
2
get IGV Reports into the workflow
#43
stevekm
opened
3 years ago
0
Make ultron_prototype primary CWL for samples fillout workflow
#42
allanbolipata
closed
3 years ago
1
get variant overlap metrics into the pipeline
#41
stevekm
opened
3 years ago
2
Ultron prototype
#40
stevekm
closed
3 years ago
1
set GetBaseCountsMultiSample to use 4 CPU's
#39
stevekm
closed
3 years ago
1
Need to deprecate `merge_mafs` method of `update_cBioPortal_data.py`
#38
stevekm
closed
3 years ago
2
Feature/increase cbioportal script mem
#37
nikhil
closed
3 years ago
0
fix Toil runner restart
#36
nikhil
closed
3 years ago
0
Feature/increase cbioportal script mem
#35
nikhil
closed
3 years ago
0
Feature/msi
#34
timosong
closed
3 years ago
3
do not run TMB on a tumor normal pair if using pooled normals
#33
stevekm
closed
3 years ago
1
Add concordance workflow & reporting
#32
stevekm
opened
3 years ago
1
Adding ram max to failing cwl
#31
allanbolipata
closed
3 years ago
0
Add ramMax to cbioportal CWL
#30
allanbolipata
closed
3 years ago
0
Deprecate CWL running methods in Makefile
#29
stevekm
closed
3 years ago
2
added merge_maf part
#28
svural
closed
4 years ago
3
add is_in_IMPACT to workflow
#27
stevekm
closed
4 years ago
1
add AF column to maf output
#26
stevekm
closed
4 years ago
1
Need parity test for new version of vcf2maf
#25
allanbolipata
closed
3 years ago
1
Shareable maf
#24
stevekm
closed
4 years ago
0
Add is in impact
#23
svural
closed
4 years ago
3
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