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Resolve milestone 2.1.0 issues#628

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Resolve milestone 2.1.0 issues#628
jscgh wants to merge 12 commits into
devfrom
milestone-2.1.0-issues

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@jscgh jscgh commented May 28, 2026 •
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Resolves #619 #209 #456 #489 #576

PR checklist

  • This comment contains a description of changes (with reason).
  • 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>).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@jscgh jscgh added this to the 2.1.0 milestone May 28, 2026
@jscgh jscgh self-assigned this May 28, 2026
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github-actions Bot commented May 28, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8551cf8

+| ✅ 349 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  31 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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
  • schema_description - No description provided in schema for parameter: rosettafold2na_uniref30_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_bfd_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_pdb100_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_weights_link
  • schema_description - No description provided in schema for parameter: rfam_full_region_link
  • schema_description - No description provided in schema for parameter: rfam_cm_link
  • schema_description - No description provided in schema for parameter: rnacentral_rfam_annotations_link
  • schema_description - No description provided in schema for parameter: rnacentral_id_mapping_link
  • schema_description - No description provided in schema for parameter: rnacentral_sequences_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_uniref30_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_bfd_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_pdb100_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_weights_path
  • local_component_structure - prepare_alphafold2_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_rosettafold2na_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_esmfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - post_processing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_alphafold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_rosettafold_all_atom_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - aria2_uncompress.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_colabfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_helixfold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_boltz_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-29 05:05:16

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jscgh commented May 28, 2026 •
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Seems the GitHub runners fail to pull the containers for #365. I'll strip out that change tomorrow.

Edit: I will increase the sharding, same as other nf-core pipelines.

@jscgh jscgh force-pushed the milestone-2.1.0-issues branch from c531231 to c428d14 Compare May 29, 2026 01:34
@jscgh jscgh force-pushed the milestone-2.1.0-issues branch from c428d14 to 1228ff1 Compare May 29, 2026 02:16
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jscgh commented May 29, 2026 •
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I've split off the CI/container changes and opened a separate PR for them (#630).

@jscgh jscgh requested a review from tlitfin May 29, 2026 02:49
@jscgh jscgh requested review from JoseEspinosa and removed request for JoseEspinosa May 29, 2026 05:59
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