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Feature: co-assemblies submission with --mode metagenomic_assembly - #66

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Feature: co-assemblies submission with --mode metagenomic_assembly#66
ochkalova wants to merge 11 commits into
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feat/coassembly_submission

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@ochkalova

@ochkalova ochkalova commented May 14, 2026 •
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Resolves #61

Allows submission of co assemblies, but not bins generated from co-assemblies.

Tests pass, some additional refactoring can be done as well as improvement of created test assertions (some files may have changing content).
What is not implemented:

  • unique sample alias for test mode for co assembly sample registration, no timestamp is added at the moment
  • calling metadata for private samples and runs (it's in TODOs for this PR)

Also a fix required for coverage calculation in ASSEMBLYSUBMIT:

// Calculate average coverage using splitCsv operator
    average_coverage_ch = COVERM_CONTIG.out.coverage
        .splitCsv(sep: '\t', skip: 1)
        .map { meta, row ->
            [meta, row[1] as Double]
        }
        .groupTuple()
        .map { meta, coverages ->
            def average = coverages.sum() / coverages.size()
            [meta, average]
        }

For co assembly CoverM output file has multiple columns, so row[1] is incorrect.

In addition it would be good to update the README with detailed explanation on how co assembly submission works.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/seqsubmit branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

ochkalova and others added 7 commits May 13, 2026 12:20
@ochkalova ochkalova changed the title Feat/coassembly submission Feature: co-assemblies submission with --mode metagenomic_assembly Jul 10, 2026
@github-actions

github-actions Bot commented Aug 5, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a9155e9

+| ✅ 257 tests passed       |+
#| ❔   9 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_dark.png
  • container_configs - container_configs

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-08-10 15:19:27

@github-actions

github-actions Bot commented Aug 5, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Aug 10, 2026 •
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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 2/7

See the full run for details.

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Co-assemblies submission support with mode "mags/bins" and "metagenomic_assemblies"

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@ochkalova