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39 Open 19 Closed
39 Open 19 Closed
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Issues list

Pipeline does not run through GATK step bug Something isn't working
#150 opened Jun 28, 2024 by KristinaGagalova
2
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
dev branch works only on the first sample bug Something isn't working
#145 opened Jun 17, 2024 by loipf
5
Test full profile is not working bug Something isn't working
#123 opened Feb 7, 2024 by nschcolnicov
2
SplitNCigarReads: sample cross-contamination bug Something isn't working
#119 opened Jan 29, 2024 by dbatrakou
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
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
2
5
Add samtools mpileup as an alternative variant caller enhancement Improvement for existing functionality
#110 opened Nov 28, 2023 by Leon-Bichmann
input file name collision bug Something isn't working
#108 opened Nov 1, 2023 by vivischuch
5
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
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
Pipeline test is failing bug Something isn't working
#89 opened Apr 10, 2023 by davidecarlson
2
strandedness field is unnecessary bug Something isn't working
#87 opened Feb 9, 2023 by bounlu
Add UMI spport enhancement Improvement for existing functionality
#86 opened Feb 9, 2023 by bounlu 1.1
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
2
ENSEMBLVEP fails after module update bug Something isn't working
#84 opened Feb 8, 2023 by bounlu
2
Warning about GATK4_HAPLOTYPECALLERGVCF bug Something isn't working
#83 opened Feb 6, 2023 by bounlu
1
SAMTOOLS_FAIDX can't locate singularity image bug Something isn't working
#82 opened Feb 2, 2023 by PBMCHUGA
9
Implementing the --AlignIntronMax option for STAR enhancement Improvement for existing functionality
#81 opened Jan 7, 2023 by ChrisSwale
1
Single cell somatic mutations enhancement Improvement for existing functionality
#77 opened Nov 22, 2022 by cutleraging
1
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