sanger-tol/sequencecomposition

Gap coordinates report

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#54 opened on Jun 4, 2026

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 (0 comments) (0 reactions) (0 assignees)Nextflow (3 forks)auto 404
enhancementgood first issueuser request

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Description

Description of feature

Run seqtk gap -l 0 to get a BED file with the gap coordinates. Send the file to bgzip, tabix, etc.

This would be the time we introduce a list of "tools" or "steps" that the user could configure

Contributor guide

Research direction
Investigate the Nextflow workflow to understand how steps are defined and parameterized, then design a configurable option to add a gap coordinates report by running `seqtk gap l 0` and processing the output with bgzip and tabix.
Tech stack
groovyshell
Domain
bioinformatics
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-2 days
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Fresh
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitNextflow
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
55