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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

OOM error for GetPileupSummaries on EC2

questionFurther information is requestedFurther information is requested

Status: Open.

#2131 In nf-core/sarek;

· georgewu1999 opened on Feb 10, 2026

Strelka2 stuck at 99% for over 24 hours (reopen)

Status: Open.

#2127 In nf-core/sarek;

· Tina04021997 opened on Feb 7, 2026

Silent failure in FASTQ_PREPROCESS_GATK for multi-lane samples (no outputs published)

bugSomething isn't workingSomething isn't working

Status: Open.

#2118 In nf-core/sarek;

· emjblake opened on Feb 1, 2026

UMI-aware Sarek

questionFurther information is requestedFurther information is requested

Status: Open.

#2114 In nf-core/sarek;

· AndreasKienzle opened on Jan 28, 2026

Join mismatch error

moreinfo

Status: Open.

#2110 In nf-core/sarek;

· anx-trade opened on Jan 20, 2026

Create a contributors guide with specifics for this pipelines

Status: Open.

#2107 In nf-core/sarek;

· FriederikeHanssen opened on Jan 20, 2026

GATK BaseRecalibrator interval usage affects variant calling

questionFurther information is requestedFurther information is requested

Status: Open.

#2097 In nf-core/sarek;

· phonegor95 opened on Jan 14, 2026

Enhance tests/variantcalling_all with all tools

Status: Open.

#2090 In nf-core/sarek;

· FriederikeHanssen opened on Jan 12, 2026

ASCAT Exome processing steps incorrect for hg38

bugSomething isn't workingSomething isn't working

Status: Open.

#2089 In nf-core/sarek;

· mheskett opened on Jan 8, 2026