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Use nft-csv to better test csv files

enhancementNew feature or requestNew feature or request

Status: Open.

#1958 In nf-core/sarek;

· maxulysse opened on Aug 19, 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

feat: Add linting of FASTQ with FQ/LINT

Status: Open (in progress).

nf-core/sareknumber 1763

#1763 In nf-core/sarek;

· adamrtalbot opened on Dec 17, 2024

Problem running Strelka due to Python version difference

bugSomething isn't workingSomething isn't working

Status: Open.

#1023 In nf-core/sarek;

· Venky2804 opened on May 15, 2023

Avoid recomputation of index in MUSE due to timestamp

Status: Open.

Task

#2024 In nf-core/sarek;

· FriederikeHanssen opened on Oct 13, 2025

Unclear docu on non-human genomes

bugSomething isn't workingSomething isn't working

docs

Status: Open.

#2022 In nf-core/sarek;

· d4straub opened on Oct 13, 2025

CNVKit Tutorial / Improved Documentation / Track issues with CNVkit

enhancementNew feature or requestNew feature or request

Status: Open.

Enhancement

#2000 In nf-core/sarek;

· FriederikeHanssen opened on Sep 29, 2025

Potentially incompatible outputs are generated with BAM output and Spark MarkDuplicates

bugSomething isn't workingSomething isn't working

Status: Open.

#1949 In nf-core/sarek;

· lbeltrame opened on Aug 5, 2025

Deepvariant requires additional cli option for recalibrated BAM files

bugSomething isn't workingSomething isn't working

Status: Open.

#682 In nf-core/sarek;

· marchoeppner opened on Jul 22, 2022

varlociraptor issues

Status: Open.

Bug

#2030 In nf-core/sarek;

· famosab opened on Oct 16, 2025

Only calculate DICT when needed

enhancementNew feature or requestNew feature or request

Status: Open.

Enhancement

#2023 In nf-core/sarek;

· FriederikeHanssen opened on Oct 13, 2025

Please add VEP plugins (Conservation and Condel)

enhancementNew feature or requestNew feature or request

Status: Open.

#1549 In nf-core/sarek;

· andrew2k opened on May 30, 2024

401 Unauthorized error from Singularity gatk

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#2040 In nf-core/sarek;

· cakirb opened on Oct 23, 2025