Important! Template update for nf-core/tools v3.2.1 #132

nf-core-bot · 2025-04-30T12:28:42Z

Version 3.2.1 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-3.2.1 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 v3.2.1 release page.

johandahlberg

@fbdtemme could you also have a look at this and see if you think everything looks ok?

johandahlberg · 2025-05-06T07:22:00Z

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

-## v1.3.1 - [date]
+## v1.5.0dev - [date]


Suggested change

## v1.5.0dev - [date]

## v1.3.1 - [date]

I am not quite sure why this change came in to the changelog, and I think we should revert it.

github-actions · 2025-05-06T11:08:26Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit e8d2792

+| ✅ 223 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

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 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!

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
actions_ci - actions_ci
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-pixelator_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-pixelator_logo_light.png
files_exist - File found: docs/images/nf-core-pixelator_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-pixelator_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowPixelator.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: validation.help.enabled
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.5.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.save_amplicon_reads= false
nextflow_config - Config default value correct: params.trim_front= 0
nextflow_config - Config default value correct: params.trim_tail= 0
nextflow_config - Config default value correct: params.max_n_bases= 0
nextflow_config - Config default value correct: params.avg_qual= 20
nextflow_config - Config default value correct: params.adapterqc_mismatches= 0.1
nextflow_config - Config default value correct: params.save_qc_passed_reads= false
nextflow_config - Config default value correct: params.save_qc_failed_reads= false
nextflow_config - Config default value correct: params.demux_mismatches= 0.1
nextflow_config - Config default value correct: params.save_demux_processed_reads= false
nextflow_config - Config default value correct: params.save_demux_failed_reads= false
nextflow_config - Config default value correct: params.algorithm= adjacency
nextflow_config - Config default value correct: params.max_neighbours= 60
nextflow_config - Config default value correct: params.collapse_mismatches= 2
nextflow_config - Config default value correct: params.collapse_min_count= 2
nextflow_config - Config default value correct: params.save_collapsed_reads= false
nextflow_config - Config default value correct: params.multiplet_recovery= true
nextflow_config - Config default value correct: params.graph_max_refinement_recursion_depth= 5
nextflow_config - Config default value correct: params.graph_max_edges_to_split= 5
nextflow_config - Config default value correct: params.graph_min_count= 2
nextflow_config - Config default value correct: params.save_edgelist= false
nextflow_config - Config default value correct: params.dynamic_filter= min
nextflow_config - Config default value correct: params.aggregate_calling= true
nextflow_config - Config default value correct: params.save_raw_component_metrics= false
nextflow_config - Config default value correct: params.save_annotate_dataset= false
nextflow_config - Config default value correct: params.compute_polarization= true
nextflow_config - Config default value correct: params.compute_colocalization= true
nextflow_config - Config default value correct: params.polarization_transformation= log1p
nextflow_config - Config default value correct: params.polarization_n_permutations= 50
nextflow_config - Config default value correct: params.polarization_min_marker_count= 5
nextflow_config - Config default value correct: params.colocalization_transformation= rate-diff
nextflow_config - Config default value correct: params.colocalization_neighbourhood_size= 1
nextflow_config - Config default value correct: params.colocalization_n_permutations= 50
nextflow_config - Config default value correct: params.colocalization_min_region_count= 5
nextflow_config - Config default value correct: params.colocalization_min_marker_count= 5
nextflow_config - Config default value correct: params.save_analysis_dataset= false
nextflow_config - Config default value correct: params.no_node_marker_counts= false
nextflow_config - Config default value correct: params.layout_algorithm= wpmds_3d
nextflow_config - Config default value correct: params.save_all= false
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - PIXELATOR found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_LIST_OPTIONS found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_COLLECT_METADATA found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_AMPLICON found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_QC found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_DEMUX found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_COLLAPSE found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_GRAPH found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_ANNOTATE found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_ANALYSIS found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_LAYOUT found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_REPORT found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.2.1

Run details

nf-core/tools version 3.2.1
Run at 2025-05-06 12:40:29

fbdtemme

Just a couple of documentation lines that have gone missing.

fbdtemme · 2025-05-06T12:21:34Z

README.md

-If you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)
+<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
+<!-- If you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->


The original needs to be kept here.

fbdtemme · 2025-05-06T12:22:01Z

README.md

-> [!WARNING]
-> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.
-> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable
-> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.


Lets keep this warning in as well.

johandahlberg · 2025-05-06T12:49:49Z

We are brining this in to dev now so that we can fix the tests in a separate PR.

nf-core-bot added 3 commits January 20, 2025 14:35

Template update for nf-core/tools version 3.1.2

9a2b63d

Template update for nf-core/tools version 3.2.0

cbc915a

Template update for nf-core/tools version 3.2.1

419381b

nf-core-bot mentioned this pull request Apr 30, 2025

Important! Template update for nf-core/tools v3.2.0 #128

Closed

johandahlberg approved these changes May 6, 2025

View reviewed changes

Merge branch 'dev' into nf-core-template-merge-3.2.1

63e6ed4

johandahlberg added 3 commits May 6, 2025 13:11

Use v4 of github cache action

bae2d5d

Bring files in line with template

1b63118

Update lint config

b6dc70d

fbdtemme requested changes May 6, 2025

View reviewed changes

Fix up README

e8d2792

fbdtemme approved these changes May 6, 2025

View reviewed changes

johandahlberg merged commit cc20d47 into dev May 6, 2025
28 of 38 checks passed

fbdtemme mentioned this pull request May 27, 2025

Release pixelator 2.0 #138

Merged

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Important! Template update for nf-core/tools v3.2.1 #132

Important! Template update for nf-core/tools v3.2.1 #132

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Important! Template update for nf-core/tools v3.2.1 #132

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️

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