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BWA index isn't coppied over with using save-reference option

Azure

bugSomething isn't workingSomething isn't working

Status: Open.

#712 In nf-core/sarek;

· vsmalladi opened on Aug 22, 2022

FILTERMUTECTCALLS is not run for tumor-only samples when there is no germline_resource

bugSomething isn't workingSomething isn't working

Status: Open.

#1546 In nf-core/sarek;

· brandenjlynch opened on May 27, 2024

Different sample name handling causes issues with merging

bugSomething isn't workingSomething isn't working

Status: Open.

#1528 In nf-core/sarek;

· njspix opened on May 16, 2024

Restart from step variantcalling fails on haplotypecaller

bugSomething isn't workingSomething isn't working

Status: Open.

#1616 In nf-core/sarek;

· FriederikeHanssen opened on Aug 8, 2024

Restart from step variantcalling fails on NGScheckmate

bugSomething isn't workingSomething isn't working

Status: Open.

#1615 In nf-core/sarek;

· FriederikeHanssen opened on Aug 8, 2024

CNVKIT doesn't accept *.list format interval files

bugSomething isn't workingSomething isn't working

input validation

Status: Open.

#1610 In nf-core/sarek;

· cmatKhan opened on Aug 2, 2024

cnvkit reference titling broken

bugSomething isn't workingSomething isn't working

Status: Open.

#1606 In nf-core/sarek;

· SethMagnusJarvis opened on Jul 31, 2024

GATK4_MARKDUPLICATES : Not a valid path value type: java.util.ArrayList

bugSomething isn't workingSomething isn't working

Status: Open.

#1598 In nf-core/sarek;

· farshadf opened on Jul 16, 2024

base.conf does not override module's process.label for CNVKIT_BATCH

bugSomething isn't workingSomething isn't working

Status: Open.

#1591 In nf-core/sarek;

· dimalvovs opened on Jul 11, 2024

Test and document that Sarek can handle input-samplesheets with mixed samples

docs

enhancementNew feature or requestNew feature or request

samplesheet

Status: Open.

#1576 In nf-core/sarek;

· asp8200 opened on Jun 25, 2024