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Multiple input files error on BAM_VARIANT_CALLING_SOMATIC_MUTECT2 fails on tumor/normal

bugSomething isn't workingSomething isn't working

Status: Open.

#1834 In nf-core/sarek;

· tanas80 opened on Mar 13, 2025

Run CRAM_TO_BAM only once per pipeline run

enhancementNew feature or requestNew feature or request

Status: Open.

#1830 In nf-core/sarek;

· famosab opened on Mar 12, 2025

single germline sample VCF quality control

enhancementNew feature or requestNew feature or request

Status: Open.

#1822 In nf-core/sarek;

· Eduardo-Auer opened on Mar 10, 2025

Convert remaining pytests to nf-test

testing

Status: Open.

#1818 In nf-core/sarek;

· famosab opened on Mar 7, 2025

Sample sheet incorrectly detected as tumor-only in germline workflow (HaplotypeCaller)

bugSomething isn't workingSomething isn't working

Status: Open.

#1813 In nf-core/sarek;

· vikramadhithyaThotam22 opened on Feb 28, 2025

Deal with trailing whitespace when snapshotting empty lists in nf-test

Status: Open.

#1807 In nf-core/sarek;

· maxulysse opened on Feb 25, 2025

Termination of the sarek process without any output

Status: Open.

#1805 In nf-core/sarek;

· BOBOL513 opened on Feb 19, 2025

NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP terminated with an error

bugSomething isn't workingSomething isn't working

Status: Open.

#1801 In nf-core/sarek;

· pnolabs opened on Feb 13, 2025

LOFTEE plugin not generating annotations in VEP output (Sarek v3.4.4)

Status: Open.

#1795 In nf-core/sarek;

· mi3112 opened on Feb 10, 2025

How can I use mutect in both tumor-only and normal mode?

Status: Open.

#1794 In nf-core/sarek;

· yannic-chen opened on Feb 10, 2025

tmp Files

bugSomething isn't workingSomething isn't working

Status: Open.

#1793 In nf-core/sarek;

· Ons14 opened on Feb 7, 2025

SAREK not producing multiQC report

bugSomething isn't workingSomething isn't working

Status: Open.

#1792 In nf-core/sarek;

· Dorothynyamai opened on Feb 7, 2025