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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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Generating flagstats for RNAseq
#108
Layth17
closed
1 year ago
1
Metrics files
#107
chrisamiller
closed
1 year ago
1
Reorganization of Immuno.wdl Outputs
#106
Layth17
closed
1 year ago
3
Reorganization of directories
#105
Layth17
closed
1 year ago
0
Exposing Variant Filtering Params
#104
Layth17
closed
10 months ago
6
Investigate intersection/annotation of "known variants" when a variant VCF from CLE for example is supplied
#103
malachig
closed
1 year ago
8
documentation updates
#102
chrisamiller
closed
1 year ago
0
Finish/Verify conversions from CWL
#101
chrisamiller
opened
1 year ago
0
Update hla_consensus.wdl to handle ambiguity codes.
#100
chrisamiller
opened
1 year ago
0
Bugfix and optimiziation for VCF filtering.
#99
tmooney
closed
1 year ago
3
increase resources for unaligned seq fda step
#98
malachig
closed
1 year ago
0
expose variant filtering params up to immuno
#97
malachig
closed
6 months ago
3
Out of resources in FDA unaligned metrics step
#96
malachig
closed
1 year ago
3
Also output the tabix index for the VCF in pvacseq workflow.
#95
tmooney
closed
1 year ago
0
Add tabix indexed file to output
#94
malachig
closed
1 year ago
1
Update WDLs for upcoming pVACtools 4.0.0 release
#93
susannasiebert
closed
1 year ago
1
Need to quote inputs in the script.
#92
tmooney
closed
1 year ago
0
increase space request to ensure bam can be created from cram
#91
malachig
closed
1 year ago
3
Out of disk error from FDA reports workflow
#90
malachig
closed
1 year ago
2
Watch out for problematic values in manually supplied metrics for FDA report
#89
malachig
closed
1 year ago
1
Minor updates to output naming and organization for immuno.wdl
#88
malachig
closed
1 year ago
1
updates to pvacseq
#87
malachig
opened
1 year ago
1
Create QC Metrics output type.
#86
tmooney
closed
1 year ago
3
Star Fusion -- relaxing FFPM filter & extracting preliminary files
#85
Layth17
closed
1 year ago
2
Relax star fusion detection parameters for filtering
#84
malachig
closed
1 year ago
2
Fix StarFusion reference bundle
#83
malachig
closed
1 year ago
1
Update star fusion detect to keep the "preliminary" fusion calls
#82
malachig
closed
1 year ago
5
Only try to look up custom annotations if we have some.
#81
tmooney
closed
1 year ago
1
Switch away from "cle" image in VCF filtering steps.
#80
tmooney
closed
1 year ago
0
Add localization optional to varscan somatic.
#79
tmooney
closed
1 year ago
1
Add FDA metrics subworkflow to Immuno pipeline
#78
tmooney
closed
1 year ago
3
Bump AGFusion docker image verison.
#77
tmooney
closed
1 year ago
0
Switch to patched version of star fusion to handle readgroup tag option.
#76
tmooney
closed
1 year ago
0
Update docker image to 0.5.4 for handling of case of 0-depth variant.
#75
tmooney
closed
1 year ago
0
added new runtime attributes to all tasks
#74
Layth17
closed
1 year ago
0
Intuitive file/input names
#73
Layth17
closed
1 year ago
0
Rename final result file: "optitype_calls.txt" to something more intuitive
#72
malachig
closed
1 year ago
0
Move specification of preemptible and maxRetries into runtime blocks of each task
#71
malachig
closed
1 year ago
1
Experiment with use of private VMs
#70
malachig
opened
1 year ago
3
Better Naming to reflect orgiin of TSV and VCF files from pvacseq subworkflow outputs.
#69
tmooney
closed
1 year ago
1
Runs failing at RNA_star_fusion's AgFusion step when no fusions are found.
#68
ksinghal28
closed
1 year ago
1
Set localization_optional on inputs for some GATK and samtools calls.
#67
tmooney
closed
1 year ago
0
Pass along the sample name to the shellscript.
#66
tmooney
closed
2 years ago
0
Fix for new shell script version of mapq0 filter from 0.5.2
#65
tmooney
closed
2 years ago
0
use localization_optional when possible
#64
chrisamiller
opened
2 years ago
3
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
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