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Add pydamage results to binqc table #835

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@jfy133 jfy133 commented Jun 22, 2025 •
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See code TODOs

To close #833

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/mag 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).

@jfy133 jfy133 linked an issue Jun 22, 2025 that may be closed by this pull request
Ancient DNA mode: Add pyDamage results to bin_summary.tsv #833
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 17a75c4

+| ✅ 360 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  48 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • local_component_structure - gtdbtk_db_preparation.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gtdbtk_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - adjust_maxbin2_ext.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - rename_predastool.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - pool_single_reads.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bowtie2_assembly_build.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bowtie2_removal_build.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bowtie2_removal_align.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - rename_postdastool.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - mag_depths.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - nanolyse.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - quast.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - split_fasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - quast_bins.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - tiara_classify.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - convert_depths.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - mag_depths_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bowtie2_assembly_align.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - pool_paired_reads.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - mag_depths_plot.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - quast_bins_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bin_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - binning.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bin_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - virus_identification.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - hybrid_assembly.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_assembly.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_assembly.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - tiara.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_binning_preparation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - ancient_dna.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_binning_preparation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - binning_refinement.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - catpack.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - assembly.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - binning_preparation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - gtdbtk.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - depths.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - domain_classification.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-22 05:08:31

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Ancient DNA mode: Add pyDamage results to bin_summary.tsv
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