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Issues list

Minimum VAF cutoff hardcoded in the Fp Filter step
#165 by evelyn-schmidt was closed Nov 14, 2024
2
Insufficient storage to complete VEP step for germline variant annotation
#162 by malachig was closed Oct 15, 2024
Out of disk error during gather bam step
#160 by malachig was closed Oct 9, 2024
3
A typo in somatic_exome_nonhuman results in the VCF tumor column being renamed to use the normal sample name
#155 by malachig was closed Oct 15, 2024
1
Produce a new variant report table customized to immuno.wdl
#137 by malachig was closed Feb 5, 2025
1
Immuno workflow annotated VCF gets written as a .vcf file instead of .vcf.gz bug Something isn't working
#126 by susannasiebert was closed Jun 27, 2023
4
Fix germline variant calling inputs for the pvactool proximal variation analysis
#125 by malachig was closed Sep 25, 2023
1
@evelyn-schmidt
2
sambamba-sort error: not enough data in stream
#120 by malachig was closed Oct 15, 2024
1
1
Rename end bias plot
#119 by malachig was closed Nov 14, 2023
1
@Layth17
1
Allow user to set a gnomad allele freq threshold for filtering enhancement New feature or request
#112 by malachig was closed Jul 10, 2023
@malachig
1
Metrics files
#107 by chrisamiller was closed Apr 7, 2023
1
@Layth17
1
Investigate intersection/annotation of "known variants" when a variant VCF from CLE for example is supplied bug Something isn't working enhancement New feature or request
#103 by malachig was closed Jul 10, 2023
@malachig
8
expose variant filtering params up to immuno enhancement New feature or request
#97 by malachig was closed Mar 7, 2024
1
@malachig @Layth17
3
Out of resources in FDA unaligned metrics step
#96 by malachig was closed Mar 24, 2023
3
Add tabix indexed file to output
#94 by malachig was closed Mar 16, 2023
1
1
Out of disk error from FDA reports workflow
#90 by malachig was closed Mar 17, 2023
2
Watch out for problematic values in manually supplied metrics for FDA report
#89 by malachig was closed Mar 16, 2023
1
@tmooney
1
Minor updates to output naming and organization for immuno.wdl enhancement New feature or request
#88 by malachig was closed Apr 7, 2023
1
@Layth17
1
Relax star fusion detection parameters for filtering
#84 by malachig was closed Mar 9, 2023
1
2
Fix StarFusion reference bundle
#83 by malachig was closed Feb 22, 2023
1
Update star fusion detect to keep the "preliminary" fusion calls
#82 by malachig was closed Mar 9, 2023
1
5
Rename final result file: "optitype_calls.txt" to something more intuitive
#72 by malachig was closed Nov 8, 2022
1
Move specification of preemptible and maxRetries into runtime blocks of each task
#71 by malachig was closed Dec 1, 2022
1
1
Better Naming to reflect orgiin of TSV and VCF files from pvacseq subworkflow outputs.
#69 by tmooney was closed Nov 8, 2022
1
1
Runs failing at RNA_star_fusion's AgFusion step when no fusions are found.
#68 by ksinghal28 was closed Feb 14, 2023
1
1
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