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Add a --query option for when there is only one query.

enhancementNew feature or requestNew feature or request

Status: Open.

#112 In nf-core/pairgenomealign;

· charles-plessy opened on May 26, 2026

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2.3.0

Labels misaligned on SVG tubemap

bugSomething isn't workingSomething isn't working

Status: Open.

#103 In nf-core/pairgenomealign;

· charles-plessy opened on Jan 27, 2026

·  

2.3.0

Output more distances from the whole alignment

enhancementNew feature or requestNew feature or request

Status: Open.

#102 In nf-core/pairgenomealign;

· charles-plessy opened on Jan 26, 2026

Allow single strand indexing.

enhancementNew feature or requestNew feature or request

Status: Open.

#97 In nf-core/pairgenomealign;

· charles-plessy opened on Oct 20, 2025

·  

2.3.0

Race condition in sequence length recording in last/align?

bugSomething isn't workingSomething isn't working

Status: Open.

#94 In nf-core/pairgenomealign;

· charles-plessy opened on Oct 6, 2025

MultiQC to include line/scatter plot

enhancementNew feature or requestNew feature or request

Status: Open.

#93 In nf-core/pairgenomealign;

· johannesnicolaus opened on Sep 9, 2025

·  

2.3.0

Increase target–query symmetry with--gapsym and --matsym.

enhancementNew feature or requestNew feature or request

Status: Open.

#91 In nf-core/pairgenomealign;

· charles-plessy opened on Sep 1, 2025

·  

3.0.0

Use CRAM 3.1

enhancementNew feature or requestNew feature or request

Status: Open.

#86 In nf-core/pairgenomealign;

· charles-plessy opened on Aug 1, 2025

·  

3.0.0

AWS full test workflow revision handling differs from nf-core standard

Status: Open.

#85 In nf-core/pairgenomealign;

· edmundmiller opened on Jul 31, 2025

VCF output support

enhancementNew feature or requestNew feature or request

Status: Open.

#82 In nf-core/pairgenomealign;

· charles-plessy opened on Jul 2, 2025

·  

2.3.0

Document at least the _target_ genome length in last/lastal report.

enhancementNew feature or requestNew feature or request

Status: Open.

#77 In nf-core/pairgenomealign;

· charles-plessy opened on May 31, 2025

·  

2.3.0

Test for file existence in nextflow_schema.json

enhancementNew feature or requestNew feature or request

Status: Open.

#73 In nf-core/pairgenomealign;

· charles-plessy opened on May 30, 2025

·  

2.3.0