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277 Open 502 Closed
277 Open 502 Closed
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Issues list

Enable Mutect2 force-calling using --alleles flag enhancement New feature or request good first issue Good for newcomers
#1883 opened May 2, 2025 by wchukwu
Create the contributors list in the nextflow.config
#1882 opened May 2, 2025 by maxulysse
GATK tooling update to fix Bug in Markduplicates
#1880 opened Apr 30, 2025 by FriederikeHanssen
1
Incomplete pre-processing when running from "--step prepare_recalibration"?
#1875 opened Apr 28, 2025 by DHelix
GATK joint variant calling with option --include-non-variant-sites fails due to GenotypeGVCFs missing intervals file input enhancement New feature or request
#1870 opened Apr 17, 2025 by percyfal
7
Refactor Sentieon preprocessing Modules into Subworkflow sentieon
#1869 opened Apr 14, 2025 by edmundmiller
Remove license file support for Sentieon sentieon
#1865 opened Apr 10, 2025 by edmundmiller
@edmundmiller
1
Q: how to deal with the fact that msisensor pro is free for non-commercial
#1861 opened Apr 4, 2025 by nh13
Duplicate test-data inputs testing
#1860 opened Apr 4, 2025 by famosab
Missing c. and p. Position in VEP Annotation & OMIM/RefSeq Intersection Issue bug Something isn't working
#1854 opened Apr 2, 2025 by vikramadhithyaThotam22
3
Sarek goes GPU - parabricks integration
#1853 opened Apr 1, 2025 by famosab
ARM pipeline run end to end
#1843 opened Mar 24, 2025 by edmundmiller
Why is the ENSEMBLVEP_VEP process not ran on chunks? enhancement New feature or request
#1840 opened Mar 22, 2025 by MahShaaban
7
Input files copied to work directory by unspecific output bug Something isn't working
#1838 opened Mar 18, 2025 by johnoooh
@johnoooh
ASCAT not running in sarek bug Something isn't working
#1837 opened Mar 17, 2025 by paumarc
3
Multiple input files error on BAM_VARIANT_CALLING_SOMATIC_MUTECT2 fails on tumor/normal bug Something isn't working moreinfo
#1834 opened Mar 13, 2025 by tanas80
4
Run CRAM_TO_BAM only once per pipeline run enhancement New feature or request
#1830 opened Mar 12, 2025 by famosab
1
single germline sample VCF quality control enhancement New feature or request
#1822 opened Mar 10, 2025 by Eduardo-Auer
5
Convert remaining pytests to nf-test testing
#1818 opened Mar 7, 2025 by famosab
18 of 27 tasks
2
Termination of the sarek process without any output moreinfo
#1805 opened Feb 19, 2025 by BOBOL513
2
How can I use mutect in both tumor-only and normal mode? question Further information is requested
#1794 opened Feb 10, 2025 by yannic-chen
4
tmp Files bug Something isn't working moreinfo
#1793 opened Feb 7, 2025 by Ons14
1
Join mismatch/DataflowVariable assignment error bug Something isn't working
#1790 opened Feb 3, 2025 by ellisjj 3.6
6
Missing Execution Report and Trace File for --step variant_annotation and --step annotate moreinfo
#1788 opened Jan 31, 2025 by hemanoel
1
GATKException: there is no usable data in any input file moreinfo
#1787 opened Jan 30, 2025 by BaderddineSaleh
3
ProTip! Exclude everything labeled bug with -label:bug.