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Workflow exits after TrimGalore with “successful” status but no alignments produced

bugSomething isn't workingSomething isn't working

Status: Open.

#589 In nf-core/methylseq;

· sansense opened on Dec 9, 2025

conflicting advice in usage document

bugSomething isn't workingSomething isn't working

Status: Open.

#588 In nf-core/methylseq;

· sansense opened on Dec 9, 2025

[bug] - samplesheet schema for genome field too strict

Status: Open.

#587 In nf-core/methylseq;

· feiloo opened on Dec 9, 2025

--aligner bwameth samtools sort bam incorrectly named with deduplicated prefix

bugSomething isn't workingSomething isn't working

Status: Open.

#580 In nf-core/methylseq;

· tylerstahl opened on Nov 29, 2025

--rrbs samtools sort bam incorrectly named with deduplicated prefix

bugSomething isn't workingSomething isn't working

Status: Open.

#579 In nf-core/methylseq;

· tylerstahl opened on Nov 28, 2025

—skip_deduplication flag does not activate duplication skipping

bugSomething isn't workingSomething isn't working

Status: Open.

#575 In nf-core/methylseq;

· kmkappa opened on Nov 7, 2025

Support multiple bed files for targeted sequencing analysis

enhancementNew feature or requestNew feature or request

Status: Open.

#573 In nf-core/methylseq;

· bounlu opened on Oct 27, 2025

Running in <code>-stub</code> mode fails for BISMARK_SUMMARY

bugSomething isn't workingSomething isn't working

Status: Open.

#527 In nf-core/methylseq;

· bounlu opened on May 9, 2025

Bismark soft clip --local_alignment True keeps L,value,value

bugSomething isn't workingSomething isn't working

Status: Open.

#472 In nf-core/methylseq;

· ioannagare opened on Nov 27, 2024

Add minimap2 as aligner option for Bismark

enhancementNew feature or requestNew feature or request

Status: Open.

#455 In nf-core/methylseq;

· FelixKrueger opened on Nov 12, 2024

Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency

enhancementNew feature or requestNew feature or request

Status: Open.

#394 In nf-core/methylseq;

· pdemko opened on Apr 1, 2024

Support for NuGEN Ovation RRBS

staleWill eventually be closed due to divergence and compatibility issues.Will eventually be closed due to divergence and compatibility issues.

Status: Open.

#376 In nf-core/methylseq;

· jma1991 opened on Jan 19, 2024