Skip to content

CHANGELOG update - #26

Merged
JeanMainguy merged 1 commit into
mainfrom
dev
Jul 31, 2026
Merged

CHANGELOG update#26
JeanMainguy merged 1 commit into
mainfrom
dev

Conversation

@JeanMainguy

@JeanMainguy JeanMainguy commented Jul 31, 2026

Copy link
Copy Markdown
Member

Update change log about license change

@github-actions

github-actions Bot commented Jul 31, 2026

Copy link
Copy Markdown

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e99e1a0

+| ✅ 223 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗  40 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 0.1.4
  • files_unchanged - LICENSE does not match the template
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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_lint - Parameter input not found in schema
  • local_component_structure - gather_pangenome_infos.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - filter_genomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - merge_gtdb_split_species.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - any2fasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - quicktree.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - metapang_index_pangenome.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - sort_genomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - mash_distance_in_phylip.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - publish_input_genomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - prepare_ppanggolin_inputs.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fasta_path_from_index.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - format_input_genomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - summarize_genome_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - md5sum_on_list_of_files.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - cluster_stat.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - cluster_plot.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - mash_sketch.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - seqfu_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - find_gtdb_split_species.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - genome_selection_from_tree.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - metapang_index_bank.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - metapang.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - genome_dereplication.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - gtdb_split.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-pangbank_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-pangbank_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-pangbank_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-pangbank_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-pangbank_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-pangbank_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/PanGBank-wf/PanGBank-wf/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-07-31 13:20:13

@JeanMainguy
JeanMainguy merged commit abbb88d into main Jul 31, 2026
4 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

1 participant

@JeanMainguy