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Issues list

replace or upgrade delly somatic analysis related to post-alignment analysis of the tumor sample
#1011 opened May 20, 2024 by anoronh4
@anoronh4
Add assay type to MultiQC output. enhancement New feature or request qc related to qc modules
#1010 opened May 2, 2024 by price0416
use Channel.interval() factory instead of watchPath backburner probably won't address in a near future
#1009 opened Apr 30, 2024 by anoronh4
1
clean up ngi-genomes folder
#1007 opened Mar 13, 2024 by anoronh4
Aggregate from Path will fail in certain aggregation process when certain samples have non-complete subworkflow enhancement New feature or request
#1002 opened Jan 26, 2024 by gongyixiao 2.0
@anoronh4
storeDir option doesn't work for all modules
#1000 opened Dec 22, 2023 by anoronh4
1
@anoronh4
1
update multiqc
#999 opened Dec 14, 2023 by anoronh4
Improvement for cohort multiqc report html
#997 opened Nov 27, 2023 by gongyixiao
brass fails when input bai file does not having the expected naming convention
#994 opened Nov 16, 2023 by anoronh4
update pipeline DAG visualization in documentation
#992 opened Oct 20, 2023 by anoronh4
Facets output incompatible with Facets Preview
#988 opened Jun 30, 2023 by anoronh4
Remove unnecessary files from SvABA published files bug Something isn't working
#982 opened Mar 30, 2023 by anoronh4
2
nextflow updates causing errors in execution bug Something isn't working
#978 opened Dec 20, 2022 by anoronh4
@anoronh4
3
SomaticCombineMutect2Vcf force sample name override header enhancement New feature or request
#976 opened Oct 3, 2022 by gongyixiao 2.0
@gongyixiao
Zygosity annotation of mutations should be done with hisens rather than purity bug Something isn't working
#967 opened Aug 23, 2022 by anoronh4 2.0
1
@anoronh4
1
Singularity runOptions add parameters to avoid loading home directory libraries for R or Python enhancement New feature or request
#938 opened Jan 25, 2022 by gongyixiao 2.0
Update oncoKB annotator version enhancement New feature or request
#936 opened Jan 22, 2022 by gongyixiao
1
Maf files from GenomeNexus enhancement New feature or request
#928 opened Dec 16, 2021 by price0416
1
QcConpair exits with error backburner probably won't address in a near future bug Something isn't working qc related to qc modules
#924 opened Sep 15, 2021 by anoronh4
@anoronh4
1
Rescue mutations that are oncogenic at 2% frequency somatic analysis related to post-alignment analysis of the tumor sample
#922 opened Sep 10, 2021 by anoronh4 2.0
1
Mutect2 column is enforced in germline calls even though mutect is not used bug Something isn't working
#916 opened Aug 25, 2021 by anoronh4 2.0
1
revise normal depth cutoff for variants enhancement New feature or request
#915 opened Aug 24, 2021 by anoronh4 2.0
1
support ora sequencing record files backburner probably won't address in a near future
#911 opened Aug 18, 2021 by anoronh4
error in GermlineCombineChannel backburner probably won't address in a near future bug Something isn't working germline analysis related to post-alignment analysis of the germline sample
#903 opened Jul 8, 2021 by anoronh4 2.0
@anoronh4
3
change input bam names of RunLOHHLA/QcQualimap/CollectHsMetrics backburner probably won't address in a near future bug Something isn't working
#892 opened Apr 26, 2021 by anoronh4
@anoronh4
2
ProTip! Exclude everything labeled bug with -label:bug.