Add gapseq modules for bacterial metabolic pathway analysis

[Copilot]

Implements nf-core modules for gapseq v1.4.0, a tool for predicting bacterial metabolic pathways and reconstructing genome-scale metabolic networks.

Modules

• gapseq/find - Pathway prediction from genomic sequences
• gapseq/findtransport - Transporter inference
• gapseq/draft - Draft metabolic model construction from pathways/transporters
• gapseq/fill - Gap filling for metabolic models
• gapseq/doall - Complete workflow wrapper (find → draft → fill)

Implementation notes

• Outputs native .tbl format (gapseq's table format, not CSV)
• Optional .fna outputs for extracted sequences
• Uses versions.yml format per current nf-core standards
• All modules use process_medium or process_high labels as appropriate
• Container: biocontainers/gapseq:1.4.0--hdfd78af_0

Example usage

include { GAPSEQ_FIND } from './modules/nf-core/gapseq/find/main'
include { GAPSEQ_DRAFT } from './modules/nf-core/gapseq/draft/main'

GAPSEQ_FIND(
    Channel.of([
        [id: 'sample1'],
        file('genome.fasta')
    ])
)

GAPSEQ_DRAFT(
    GAPSEQ_FIND.out.tbl.join(transporter_tbl)
)

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• api.anaconda.org
  • Triggering command: /usr/bin/curl curl -s REDACTED (dns block)
• gapseq.readthedocs.io
  • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)
• get.nextflow.io
  • Triggering command: /usr/bin/curl curl -s REDACTED (dns block)
  • Triggering command: /usr/bin/curl curl -fsSL REDACTED (dns block)
• nf-co.re
  • Triggering command: /home/REDACTED/.local/bin/nf-core nf-core --version (dns block)
  • Triggering command: /home/REDACTED/.local/bin/nf-core nf-core modules create --help (dns block)
  • Triggering command: /home/REDACTED/.local/bin/nf-core nf-core modules create gapseq/find --author @copilot --conda-name gapseq --conda-package-version 1.4.0 --force (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

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This section details on the original issue you should resolve

<issue_title>new module: TOOL/SUBTOOL</issue_title>
<issue_description>### Is there an existing module for this?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Further Information

Developind nf-core module for gapseq. Description of gapseq from the developers github page:
gapseq is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation. Based on genomic information and databases for pathways and reactions, gapseq can be used for:

prediction of metabolic pathways from various databases
transporter inference
metabolic model construction
multi-step gap filling

Are you going to work on this?

• If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes new module: gapseq #9619

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