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wustl-oncology
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analysis-wdls
Scalable genomic analysis pipelines, written in WDL
MIT License
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use localization_optional when possible
#64
chrisamiller
opened
2 years ago
4
Add use of monitoring script to cromwell runs
#63
malachig
opened
2 years ago
3
Also run the WDL verify script on pull requests.
#62
tmooney
closed
2 years ago
0
Upgrade mapq0 filter to v0.5.3.
#61
tmooney
closed
2 years ago
0
Handling HLA Empty Fields.
#60
Layth17
closed
2 years ago
0
Handling HLA empty fields
#59
Layth17
closed
2 years ago
0
Optimizing Optitype
#58
Layth17
closed
2 years ago
1
Adding Class II HLA typing to immuno
#57
Layth17
closed
2 years ago
3
Optimize Optitype resource usage
#56
malachig
closed
2 years ago
3
Adding Class II HLA typing to immuno
#55
Layth17
closed
2 years ago
0
array type issue
#54
Layth17
closed
2 years ago
0
Rnaseq
#53
sridhar0605
closed
2 years ago
1
approach 2 to issue #29
#52
Layth17
closed
2 years ago
2
optimize mark_duplicates_and_sort
#51
chrisamiller
opened
2 years ago
1
Gracefully handle partial optitype HLA typing
#50
malachig
closed
2 years ago
5
Fixes necessary for somatic WGS to run
#49
chrisamiller
closed
2 years ago
0
somatic wgs does not include gnomad filtering
#48
chrisamiller
opened
2 years ago
1
use localized copy of vep custom inputs
#47
chrisamiller
closed
2 years ago
1
Add fastq step and an overall immuno QC report that meets FDA NGS requirements
#46
malachig
closed
1 year ago
2
run bam QC metrics in parallel with detect variants
#45
chrisamiller
closed
2 years ago
1
Organize outputs into structs where appropriate
#44
chrisamiller
opened
2 years ago
2
add fusion results, strand test results, etc. to immuno results
#43
malachig
closed
2 years ago
1
removing bigwig creation
#42
chrisamiller
closed
2 years ago
2
reduces mutect mem to what's actually needed
#41
chrisamiller
closed
2 years ago
0
Cost optimization
#40
chrisamiller
closed
2 years ago
0
changes all tools to use HDD instead of SSD
#39
chrisamiller
closed
2 years ago
0
investigate using RNA-STAR alignment results as input for RNA-STARfusion calling
#38
malachig
closed
2 years ago
1
Add class II HLA typing to immuno analysis
#37
malachig
closed
2 years ago
1
Explore streaming sequence to Fastq and/or trimFastq steps
#36
chrisamiller
opened
2 years ago
2
remove rnaseqStarFusion.cgpbigwigBamCoverage step
#35
chrisamiller
closed
2 years ago
0
Swap SSD for HDD where possible
#34
chrisamiller
closed
2 years ago
0
optimize CPU/RAM requests
#33
chrisamiller
opened
2 years ago
2
define RNAseq results as outputs in immuno.wdl
#32
chrisamiller
closed
2 years ago
2
remove redundant alignments in immuno.wdl
#31
chrisamiller
opened
2 years ago
0
In call-ps (pvacseq) step, make sure index is newer than VCF to avoid many warnings
#30
malachig
closed
2 years ago
3
Update immuno.wdl to include a step that runs HLA typing on the tumor exome data
#29
malachig
closed
2 years ago
2
Add pvacfuse and match immuno.cwl main
#28
johnmaruska
closed
2 years ago
0
Immuno rnaseq fusion enhancements
#27
johnmaruska
closed
2 years ago
0
Benchmark different parallelization approaches to mutect
#26
johnmaruska
opened
2 years ago
0
Automate process for tagged releases
#25
johnmaruska
opened
2 years ago
0
Copy analysis-workflows relevant docstrings/comments
#24
johnmaruska
opened
2 years ago
0
Consolidate tasks+workflows definitions where reasonable
#23
johnmaruska
opened
2 years ago
0
Catch up to workflows main
#22
johnmaruska
closed
2 years ago
1
Add mark dup changes
#21
johnmaruska
closed
2 years ago
0
Add indexes cnvkit batch
#20
johnmaruska
closed
2 years ago
0
Explicitly pass in .bai files to cnvkitBatch
#19
johnmaruska
closed
2 years ago
0
Add GitHub Actions to verify and build repo
#18
johnmaruska
closed
2 years ago
0
update command so that false is passed in correct position
#17
malachig
closed
2 years ago
0
if we are going to pick a gnomad filter gnomADe_AF is more in line wi…
#16
malachig
closed
2 years ago
1
add reference.alts as an input throughout pipelines that involve alig…
#15
malachig
closed
2 years ago
0
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