wustl-oncology analysis-wdls issues

wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL

MIT License

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issues

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fix typo in naming of samples in vcf in strelka variant detection

#156 malachig closed 1 day ago
0
A typo in somatic_exome_nonhuman results in the VCF tumor column being renamed to use the normal sample name

#155 malachig opened 1 day ago
1
Troubleshoot failures during localization step

#154 malachig opened 2 days ago
1
increase memory resources to accommodate BigMHC

#153 malachig closed 5 days ago
0
Upgrade to pVACtools version 4.3.0

#152 susannasiebert closed 2 weeks ago
0
Create a tool that aggregates and prioritizes/filters fusion neoantigens

#151 malachig opened 1 month ago
1
add crai index files to the outputs

#150 malachig closed 1 month ago
0
Upgrade to pVACtools version 4.2.1

#149 susannasiebert closed 2 weeks ago
0
Change hisat2_align.wdl and update workflow.zip

#148 mhoang22 closed 1 week ago
0
Upgrade to pVACtools version 4.2.0

#147 susannasiebert closed 2 months ago
0
Add HLA LOH analysis to immuno workflow

#146 malachig opened 6 months ago
0
Upgrade to pVACtools version 4.1.0

#145 susannasiebert closed 5 months ago
0
Upgrade to pVACtools version 4.0.8

#144 susannasiebert closed 6 months ago
0
Upgrade to pVACtools version 4.0.7

#143 susannasiebert closed 7 months ago
0
Detect variant

#142 sridhar0605 opened 8 months ago
0
adding somatic wgs to dockstore

#141 sridhar0605 opened 8 months ago
1
Giving pVACseq output files unique names

#140 evelyn-schmidt opened 9 months ago
0
changing localization_optional to false in mutect tool

#139 evelyn-schmidt closed 1 week ago
6
Upgrade to pVACtools version 4.0.6

#138 susannasiebert closed 9 months ago
1
Produce a new variant report table customized to immuno.wdl

#137 malachig opened 10 months ago
0
Variant Parameter Cleanup (from PR#110)

#136 tmooney closed 9 months ago
1
Upgrade to version 5.1.0

#135 susannasiebert closed 9 months ago
4
changed star fusion cpus to 24 and turned off preempting

#134 evelyn-schmidt closed 9 months ago
1
moved the set -o lines under the ACCESS_TOKEN block

#133 evelyn-schmidt closed 9 months ago
1
Upgrade to pVACtools version 4.0.5

#132 susannasiebert closed 11 months ago
2
pvacseq/pvacfuse hangs and fails to complete

#131 rkageyama opened 11 months ago
2
renaming qc metrics chart

#130 Layth17 closed 9 months ago
1
Upgrade to pVACtools version 4.0.3

#129 susannasiebert closed 1 year ago
0
125 fix germline variant calling

#128 evelyn-schmidt closed 11 months ago
2
Update to pVACtools 4.0.1 release candidate for testing

#127 susannasiebert closed 1 year ago
2
Immuno workflow annotated VCF gets written as a .vcf file instead of .vcf.gz

#126 susannasiebert closed 1 year ago
4
Fix germline variant calling inputs for the pvactool proximal variation analysis

#125 malachig closed 11 months ago
2
Improve selection of variant annotation for the variants.tsv

#124 malachig opened 1 year ago
1
Update to official 4.0.0 pVACtools release

#123 susannasiebert closed 1 year ago
0
add MIT license to match CWL source for these pipelines

#122 malachig closed 1 year ago
0
Increase space_needed_gb in mark_duplicates_and_sort (Issue #120)

#121 ksinghal28 closed 1 year ago
0
sambamba-sort error: not enough data in stream

#120 malachig opened 1 year ago
1
Rename end bias plot

#119 malachig closed 9 months ago
1
Add orcid for apaul7.

#118 tmooney closed 1 year ago
0
Update to latest release candidate docker container

#117 susannasiebert closed 1 year ago
3
Add dockstore yml

#116 tmooney closed 1 year ago
0
Add Arriba (and respective pVACfuse step) to the immuno workflow

#115 susannasiebert opened 1 year ago
2
remove intersect_known_variants and rename filter_known_variants

#114 malachig closed 1 year ago
2
surface gnomad filter threshold to somatic and immuno workflows

#113 malachig closed 1 year ago
2
Allow user to set a gnomad allele freq threshold for filtering

#112 malachig closed 1 year ago
1
use pipe instead of redirection for varscan

#111 malachig closed 1 year ago
3
variant filtering parameter cleanup

#110 malachig closed 9 months ago
2
Investigate inconsistent variant results from varscan when using localization_optional

#109 malachig opened 1 year ago
2
Generating flagstats for RNAseq

#108 Layth17 closed 1 year ago
1
Metrics files

#107 chrisamiller closed 1 year ago
1