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Important! Template update for nf-core/tools v3.5.1#105

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nf-core-template-merge-3.5.1
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Important! Template update for nf-core/tools v3.5.1#105
nf-core-bot wants to merge 2 commits intodevfrom
nf-core-template-merge-3.5.1

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@nf-core-bot nf-core-bot commented Nov 20, 2025

Version 3.5.1 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2025/tools-3_5_0

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.5.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.5.1 release page.

Note

Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.

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github-actions Bot commented Jan 21, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 160e3ef

+| ✅ 240 tests passed       |+
#| ❔   3 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  36 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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!
  • local_component_structure - write_seqinfo.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_orthologs.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - make_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - make_score_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - make_hits_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_oma_group_local.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - filter_hits.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_inspector_group_online.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_eggnog_group_local.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_oma_group_online.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_panther_group_online.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_refseq_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - stats2csv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - filter_fasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - make_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - split_taxids.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_uniprot_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - dump_params.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_ensembl_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_ensembl_idmap.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_oma_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - split_id_format.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - make_merge_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - identify_seq_online.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fetch_panther_group_local.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - report.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - get_sequences.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - merge_ids.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - get_orthologs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - score_orthologs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-reportho_logo_light.png

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-21 12:44:21

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@nf-core-bot @mashehu