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Jobs keeps failing during GatherBQSRReports

bugSomething isn't workingSomething isn't working

Status: Open.

#2166 In nf-core/sarek;

· lucafynn opened on Apr 7, 2026

Jobs failing during CNVKIT_BATCH

Status: Open.

#2163 In nf-core/sarek;

· matt-gust opened on Mar 30, 2026

Error Manta WGS

bugSomething isn't workingSomething isn't working

moreinfo

Status: Open.

#2158 In nf-core/sarek;

· LauraRuffoni opened on Mar 18, 2026

CRAM corruption and unexpected behavior when a BGZIP-compressed reference is used

bugSomething isn't workingSomething isn't working

Status: Open.

#2157 In nf-core/sarek;

· itrujnara opened on Mar 18, 2026

Automatic ASCAT reference file generation for WES

enhancementNew feature or requestNew feature or request

Status: Open.

#2155 In nf-core/sarek;

· mheskett opened on Mar 12, 2026

vep plugin for mastermind missing adding vep_extra file in main.nf

bugSomething isn't workingSomething isn't working

Status: Open.

#2150 In nf-core/sarek;

· sicotteh opened on Feb 26, 2026

while giving --save_output_as_bam, it skips APPLYBQSR and downstream analysis

bugSomething isn't workingSomething isn't working

Status: Open.

#2149 In nf-core/sarek;

· jdabhi-0545 opened on Feb 26, 2026

Converted BAM files ar published even when -save_output_as_bam is not set

bugSomething isn't workingSomething isn't working

Status: Open.

#2148 In nf-core/sarek;

· FriederikeHanssen opened on Feb 24, 2026

Enable CombineGVCFs if no intervals are provided as fallback to GenomicsDB

Status: Open.

#2145 In nf-core/sarek;

· FriederikeHanssen opened on Feb 23, 2026

Constant OOM error for GetPileupSummaries on EC2

bugSomething isn't workingSomething isn't working

Status: Open.

#2140 In nf-core/sarek;

· georgewu1999 opened on Feb 12, 2026

Error "Detected join operation duplicate emission on left channel" when using "--save_output_as_bam" on WGS data

Status: Open.

#2136 In nf-core/sarek;

· ahwanpandey opened on Feb 11, 2026

Cram still beign created in the "work folder" even if I don't need to it be created i.e. used "save_output_as_bam"

Status: Open.

#2132 In nf-core/sarek;

· ahwanpandey opened on Feb 10, 2026