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Feat/coassembly submission#66

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Feat/coassembly submission#66
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feat/coassembly_submission

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@ochkalova ochkalova commented May 14, 2026

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.
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

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
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co-assemblies support

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