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285 Open 473 Closed
285 Open 473 Closed
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Issues list

Multiple input files error on BAM_VARIANT_CALLING_SOMATIC_MUTECT2 fails on tumor/normal bug Something isn't working
#1834 opened Mar 13, 2025 by tanas80
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
2
Convert remaining pytests to nf-test testing
#1818 opened Mar 7, 2025 by famosab
8 of 27 tasks
2
Sample sheet incorrectly detected as tumor-only in germline workflow (HaplotypeCaller) bug Something isn't working
#1813 opened Feb 28, 2025 by vikramadhithyaThotam22
6
Deal with trailing whitespace when snapshotting empty lists in nf-test
#1807 opened Feb 25, 2025 by maxulysse
Termination of the sarek process without any output
#1805 opened Feb 19, 2025 by BOBOL513
2
NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP terminated with an error bug Something isn't working
#1801 opened Feb 13, 2025 by pnolabs
@SPPearce
7
LOFTEE plugin not generating annotations in VEP output (Sarek v3.4.4)
#1795 opened Feb 10, 2025 by mi3112
1
How can I use mutect in both tumor-only and normal mode?
#1794 opened Feb 10, 2025 by yannic-chen
1
tmp Files bug Something isn't working
#1793 opened Feb 7, 2025 by Ons14
1
SAREK not producing multiQC report bug Something isn't working
#1792 opened Feb 7, 2025 by Dorothynyamai
Join mismatch/DataflowVariable assignment error bug Something isn't working
#1790 opened Feb 3, 2025 by ellisjj
5
Disabled mpileup of nfcore_sarek pipeline bug Something isn't working
#1789 opened Feb 3, 2025 by VivianRobin
3
Missing Execution Report and Trace File for --step variant_annotation and --step annotate bug Something isn't working
#1788 opened Jan 31, 2025 by hemanoel
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS'
#1787 opened Jan 30, 2025 by BaderddineSaleh
2
Join mismatch
#1786 opened Jan 30, 2025 by zbaida-achraf
3
parabricks implementation status enhancement New feature or request
#1784 opened Jan 28, 2025 by TonyKess
1
Unknown method invocation getFileSystem on LinkedList type when running Sarek
#1781 opened Jan 27, 2025 by BaderddineSaleh
1
How to prevent ApplyBQSR from passing intervals to prevent it from dropping reads.
#1772 opened Jan 15, 2025 by Mani-varma1
2
How to specify ploidy for HaplotypeCaller in the nf-core/sarek pipeline? question Further information is requested
#1771 opened Jan 13, 2025 by koraykaplan88
4
mutect2-realigned .bam output enhancement New feature or request
#1766 opened Jan 7, 2025 by seedgeorge
1
Need help! Sifting through mutations in other cell lines (parameters and tools)
#1762 opened Dec 17, 2024 by mggrami
Check that GZI index provided if using a gzipped FASTA enhancement New feature or request
#1741 opened Nov 29, 2024 by pontushojer
2
The sample-sheet only contains normal-samples error bug Something isn't working
#1740 opened Nov 25, 2024 by ashpsnair
2
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