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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

annotation step skip

enhancementNew feature or requestNew feature or request

Status: Open.

#1796 In nf-core/sarek;

· Eduardo-Auer opened on Feb 11, 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

Join mismatch/DataflowVariable assignment error

bugSomething isn't workingSomething isn't working

Status: Open.

#1790 In nf-core/sarek;

· ellisjj opened on Feb 3, 2025

Disabled mpileup of nfcore_sarek pipeline

bugSomething isn't workingSomething isn't working

Status: Open.

#1789 In nf-core/sarek;

· VivianRobin opened on Feb 3, 2025

Missing Execution Report and Trace File for --step variant_annotation and --step annotate

bugSomething isn't workingSomething isn't working

Status: Open.

#1788 In nf-core/sarek;

· hemanoel opened on Jan 31, 2025

ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS'

Status: Open.

#1787 In nf-core/sarek;

· BaderddineSaleh opened on Jan 30, 2025

Join mismatch

Status: Open.

#1786 In nf-core/sarek;

· zbaida-achraf opened on Jan 30, 2025

params.known_indels curly braces error

bugSomething isn't workingSomething isn't working

Status: Open.

#1785 In nf-core/sarek;

· allyssonallan opened on Jan 28, 2025