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Important! Template update for nf-core/tools v3.3.1#823

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jfy133 merged 17 commits intodevfrom
nf-core-template-merge-3.3.1
Jun 11, 2025
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Important! Template update for nf-core/tools v3.3.1#823
jfy133 merged 17 commits intodevfrom
nf-core-template-merge-3.3.1

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@nf-core-bot nf-core-bot commented Jun 3, 2025

Version 3.3.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.3.1 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 v3.3.1 release page.

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dialvarezs commented Jun 4, 2025

@nf-core-bot fix linting

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github-actions bot commented Jun 4, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1873af6

+| ✅ 354 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  48 tests had warnings |!
Details

❗ 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 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
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • local_component_structure - quast_bins.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 - 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 - quast_bins_summary.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 - rename_predastool.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 - mag_depths_plot.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 - gtdbtk_db_preparation.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 - nanolyse.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 - adjust_maxbin2_ext.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 - pool_paired_reads.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 - split_fasta.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 - convert_depths.nf in modules/local should be moved to a TOOL/SUBTOOL/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 - longread_hostremoval.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 - binning_preparation.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 - assembly.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 - binning.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 - bin_qc.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 - virus_identification.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 - shortread_assembly.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 - binning_refinement.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 - hybrid_assembly.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 2025-06-11 11:11:35

@jfy133
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jfy133 commented Jun 11, 2025

@nf-core-bot fix linting

jfy133
jfy133 reviewed Jun 11, 2025
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jfy133
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jfy133
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@jfy133 jfy133 moved this to Needs review in meta-omics nf-test fest Jun 11, 2025
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jfy133 commented Jun 11, 2025

@nf-core-bot fix linting

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jfy133 commented Jun 11, 2025

Tests are expected to fail, as no snapshot is generated yet. I will do that in the next PR

d4straub
d4straub approved these changes Jun 11, 2025
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LGTM, I dont see any problem.

@jfy133 jfy133 moved this from Needs review to Under Review in meta-omics nf-test fest Jun 11, 2025
@sofstam sofstam self-requested a review June 11, 2025 11:04
sofstam
sofstam approved these changes Jun 11, 2025
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changelog? :D

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jfy133 commented Jun 11, 2025

Tahnk you @sofstam !

@jfy133 jfy133 merged commit e050f1c into dev Jun 11, 2025
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@github-project-automation github-project-automation bot moved this from Under Review to Done in meta-omics nf-test fest Jun 11, 2025
@dialvarezs dialvarezs deleted the nf-core-template-merge-3.3.1 branch November 21, 2025 11:36
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@jfy133 jfy133 jfy133 left review comments

@d4straub d4straub d4straub approved these changes

@sofstam sofstam sofstam approved these changes

@prototaxites prototaxites Awaiting requested review from prototaxites prototaxites is a code owner

@muabnezor muabnezor Awaiting requested review from muabnezor muabnezor is a code owner

@dialvarezs dialvarezs Awaiting requested review from dialvarezs dialvarezs is a code owner

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