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33 Open 27 Closed
33 Open 27 Closed
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Issues list

vep cache version: Value is [integer] but should be [string] bug Something isn't working
#163 opened Feb 11, 2025 by ecapriotti 1.2.0
1
Permissions Error in STAR Align Step bug Something isn't working
#162 opened Feb 6, 2025 by tpham2654 1.2.0
@nvnieuwk
1
Thoughts on submitting RNAVar to a journal? question Further information is requested
#147 opened Jun 26, 2024 by Shaun-Regenbaum
Add a bgzip module for dbsnp files enhancement Improvement for existing functionality
#146 opened Jun 25, 2024 by nschcolnicov 1.2.0
Test full profile is not working bug Something isn't working
#123 opened Feb 7, 2024 by nschcolnicov 1.2.0
2
It is possible to make "known indels" and "dbsnp" databases optional in this pipeline as was done in Sarek? enhancement Improvement for existing functionality
#118 opened Jan 26, 2024 by Jokendo-collab 1.2.0
3
Failure on GATK4_BEDTOINTERVALLIST due to incorrect exome.bed generation from iGenomes References. bug Something isn't working
#112 opened Dec 26, 2023 by Shaun-Regenbaum 1.2.0
2
5
Add samtools mpileup as an alternative variant caller enhancement Improvement for existing functionality
#110 opened Nov 28, 2023 by Leon-Bichmann
dev version gets stuck at Launching step bug Something isn't working
#103 opened Oct 12, 2023 by bounlu
Add trimming step enhancement Improvement for existing functionality
#96 opened Aug 15, 2023 by bounlu
STAR_ALIGN error "Not a valid S3 file system provider file attribute view: java.nio.file.attribute.BasicWithKeyFileAttributeView" bug Something isn't working
#94 opened Jun 6, 2023 by BurtonChia 1.2.0
1
Singularity container retrieval failed bug Something isn't working
#93 opened Jun 1, 2023 by hakobyansiras
Genome Version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a bug Something isn't working
#92 opened May 31, 2023 by meherpreethi777
8
GRCh38 gtf file being used even when custom gff file is supplied bug Something isn't working
#90 opened Apr 11, 2023 by davidecarlson 1.2.0
Pipeline test is failing bug Something isn't working
#89 opened Apr 10, 2023 by davidecarlson 1.2.0
2
strandedness field is unnecessary bug Something isn't working
#87 opened Feb 9, 2023 by bounlu 1.2.0
Add UMI spport enhancement Improvement for existing functionality
#86 opened Feb 9, 2023 by bounlu 1.2.0
ANNOTATE processes scheduled but not executed despite params.annotate_tool not null and skip_variantannotation = false bug Something isn't working
#85 opened Feb 8, 2023 by PBMCHUGA 1.2.0
2
ENSEMBLVEP fails after module update bug Something isn't working
#84 opened Feb 8, 2023 by bounlu 1.2.0
2
Warning about GATK4_HAPLOTYPECALLERGVCF bug Something isn't working
#83 opened Feb 6, 2023 by bounlu 1.2.0
1
SAMTOOLS_FAIDX can't locate singularity image bug Something isn't working
#82 opened Feb 2, 2023 by PBMCHUGA 1.2.0
9
Implementing the --AlignIntronMax option for STAR enhancement Improvement for existing functionality
#81 opened Jan 7, 2023 by ChrisSwale 1.2.0
1
Single cell somatic mutations enhancement Improvement for existing functionality
#77 opened Nov 22, 2022 by cutleraging
1
Prepared STARIndex folder is missing for GATK/GRCh38 bug Something isn't working
#74 opened Oct 10, 2022 by bounlu 1.2.0
NFCORE_RNAVAR:RNAVAR:SPLITNCIGAR:GATK4_SPLITNCIGARREADS error bug Something isn't working
#72 opened Oct 2, 2022 by gianfilippo 1.2.0
3
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