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Bump samtools in cnvkit

Status: Open.

#1895 In nf-core/sarek;

· FriederikeHanssen opened on May 19, 2025

Missing conversion from bam to cram when starting from "--step prepare_recalibration"

bugSomething isn't workingSomething isn't working

Status: Open.

#1894 In nf-core/sarek;

· alexnater opened on May 14, 2025

 ·  

3.6

Add option to run GATK FilterByOrientationBias

enhancementNew feature or requestNew feature or request

Status: Open.

Enhancement

#1893 In nf-core/sarek;

· robsyme opened on May 13, 2025

Patched Sentieon with Sarek

bugSomething isn't workingSomething isn't working

Status: Open.

#1891 In nf-core/sarek;

· um-pdavila opened on May 12, 2025

bwa mem in sarek does not align to ALT chromosomes

Status: Open.

#1889 In nf-core/sarek;

· mggrami opened on May 9, 2025

Enable Mutect2 force-calling using --alleles flag

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

Status: Open.

Enhancement

#1883 In nf-core/sarek;

· wchukwu opened on May 2, 2025

Create the contributors list in the nextflow.config

Status: Open.

#1882 In nf-core/sarek;

· maxulysse opened on May 2, 2025

GATK tooling update to fix Bug in Markduplicates

Status: Open.

#1880 In nf-core/sarek;

· FriederikeHanssen opened on Apr 30, 2025

Incomplete pre-processing when running from "--step prepare_recalibration"?

Status: Open.

Bug

#1875 In nf-core/sarek;

· DHelix opened on Apr 28, 2025

 ·  

3.6

GATK joint variant calling with option --include-non-variant-sites fails due to GenotypeGVCFs missing intervals file input

enhancementNew feature or requestNew feature or request

Status: Open.

Enhancement

#1870 In nf-core/sarek;

· percyfal opened on Apr 17, 2025

Refactor Sentieon preprocessing Modules into Subworkflow

sentieon

Status: Open.

Enhancement

#1869 In nf-core/sarek;

· edmundmiller opened on Apr 14, 2025

Remove license file support for Sentieon

sentieon

Status: Open.

Enhancement

#1865 In nf-core/sarek;

· edmundmiller opened on Apr 10, 2025