Update to nf-core 3.5.1 #450

weaglesBio · 2025-12-01T11:03:04Z

PR checklist

Update nf-core version to 3.5.1

Dev2Main

Fix for pretext file output

github-actions · 2025-12-01T11:06:11Z

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

Posted for pipeline commit 80bd157

+| ✅ 222 tests passed       |+
#| ❔  29 tests were ignored |#
!| ❗  10 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.4.4
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 base.config: Check the defaults for all processes
pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
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!
system_exit - System.exit in treeval.nf: System.exit(1) [line 116]
system_exit - System.exit in treeval.nf: System.exit(1) [line 123]

❔ Tests ignored:

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: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
files_exist - File is ignored: CODE_OF_CONDUCT.md
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-treeval_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-treeval_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-treeval_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml
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: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.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/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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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: conf/modules.config
files_exist - File found: conf/test.config
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: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: conf/base.config
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-treeval_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/WorkflowTreeval.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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.split_telomere= 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/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) strings found
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: 'application/x-yaml'
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.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: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.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.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_MERGE found in conf/base.config and Nextflow scripts.
base_config - BEDTOOLS_SORT found in conf/base.config and Nextflow scripts.
base_config - SELFCOMP_ALIGNMENTBLOCKS found in conf/base.config and Nextflow scripts.
base_config - BEDTOOLS_GENOMECOV found in conf/base.config and Nextflow scripts.
base_config - MUMMER found in conf/base.config and Nextflow scripts.
base_config - UCSC_BEDGRAPHTOBIGWIG found in conf/base.config and Nextflow scripts.
base_config - CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT found in conf/base.config and Nextflow scripts.
base_config - CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT found in conf/base.config and Nextflow scripts.
base_config - SNAPSHOT_SRES found in conf/base.config and Nextflow scripts.
base_config - PRETEXTMAP_STANDRD found in conf/base.config and Nextflow scripts.
base_config - PRETEXTMAP_HIGHRES found in conf/base.config and Nextflow scripts.
base_config - PRETEXT_GRAPH found in conf/base.config and Nextflow scripts.
base_config - JUICER_TOOLS_PRE found in conf/base.config and Nextflow scripts.
base_config - BWAMEM2_INDEX found in conf/base.config and Nextflow scripts.
base_config - MINIMAP2_INDEX found in conf/base.config and Nextflow scripts.
base_config - BAMTOBED_SORT found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_MARKDUP found in conf/base.config and Nextflow scripts.
base_config - COOLER_CLOAD found in conf/base.config and Nextflow scripts.
base_config - MERQURYFK_MERQURYFK found in conf/base.config and Nextflow scripts.
base_config - BUSCO_BUSCO found in conf/base.config and Nextflow scripts.
base_config - BUSCO_BUSCO found in conf/base.config and Nextflow scripts.
base_config - FASTK_FASTK found in conf/base.config and Nextflow scripts.
base_config - UCSC_BEDTOBIGBED found in conf/base.config and Nextflow scripts.
base_config - TABIX_BGZIPTABIX found in conf/base.config and Nextflow scripts.
base_config - GAWK_GAP_LENGTH found in conf/base.config and Nextflow scripts.
base_config - GET_PAIRED_CONTACT_BED found in conf/base.config and Nextflow scripts.
base_config - WINDOWMASKER_MKCOUNTS found in conf/base.config and Nextflow scripts.
base_config - WINDOWMASKER_USTAT found in conf/base.config and Nextflow scripts.
base_config - BEDTOOLS_INTERSECT found in conf/base.config and Nextflow scripts.
base_config - GENERATE_CRAM_CSV found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - GENERATE_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - PAF2BED found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_REFORMAT_INTERSECT found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXT_INGEST_HIRES found in conf/modules.config and Nextflow scripts.
modules_config - MERQURYFK_MERQURYFK found in conf/modules.config and Nextflow scripts.
modules_config - FASTK_FASTK found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_UPPER_SEQUENCE found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_CLEAN_TELOMERE found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_MAP_TELO found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_GAP_LENGTH found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_REPLACE_DOTS found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_RENAME_IDS found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_REFORMAT_INTERSECT found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_EXTRACT_BUSCOGENE found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_SPLIT_DIRECTIONS found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_A found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_B found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT_C found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MAKEWINDOWS found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_INTERSECT found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MAP found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_CUTN found in conf/modules.config and Nextflow scripts.
modules_config - MINIPROT_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SPLIT_REF found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SPLIT_QUERY found in conf/modules.config and Nextflow scripts.
modules_config - FIND_TELOMERE_REGIONS found in conf/modules.config and Nextflow scripts.
modules_config - FIND_TELOMERE_WINDOWS found in conf/modules.config and Nextflow scripts.
modules_config - TABIX_BGZIPTABIX found in conf/modules.config and Nextflow scripts.
modules_config - BUSCO_BUSCO found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXTMAP_STANDRD found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXTMAP_HIGHRES found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXT_INGEST_SNDRD found in conf/modules.config and Nextflow scripts.
modules_config - PRETEXT_INGEST_HIRES found in conf/modules.config and Nextflow scripts.
modules_config - YAHS found in conf/modules.config and Nextflow scripts.
modules_config - SNAPSHOT_SRES found in conf/modules.config and Nextflow scripts.
modules_config - JUICER_TOOLS_PRE found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_CLOAD found in conf/modules.config and Nextflow scripts.
modules_config - MERQURYFK_MERQURYFK 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2025-12-01 14:00:45

prototaxites

Hi Will, looking good - couple of small issues needing fixed.

prototaxites · 2025-12-01T11:12:26Z

assets/schema_input.json

@@ -1,37 +1,31 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/sanger-tol/treeval/master/assets/schema_input.json",


You overwrote your local changes to schema_input.json

prototaxites · 2025-12-01T11:13:35Z

tests/nextflow.config

 ========================================================================================
 */

+<<<<<<< HEAD


merge markers need sorting

DLBPointon and others added 7 commits November 10, 2025 20:16

Merge pull request #445 from sanger-tol/dev

53b5757

Dev2Main

Fix for pretext file output

abf44da

Adding naming

897916e

Update pretext output and test snapshot

e13cbae

Merge pull request #449 from sanger-tol/patch

4b12e7d

Fix for pretext file output

Template update for nf-core/tools version 3.5.1

8c2ae8c

fix merges

ac36a2b

prototaxites reviewed Dec 1, 2025

View reviewed changes

Feedback fixes

852a3af

prototaxites approved these changes Dec 1, 2025

View reviewed changes

weaglesBio added 4 commits December 1, 2025 12:05

Linting fix

eda7a99

Added missing comma

1970e71

Update genomecov module

3a7352a

Revert intersect module hash

80bd157

weaglesBio merged commit 75e0d13 into dev Dec 1, 2025
7 checks passed

weaglesBio deleted the template_3_5_1 branch December 1, 2025 14:33

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Update to nf-core 3.5.1 #450

Update to nf-core 3.5.1 #450

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Update to nf-core 3.5.1 #450

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weaglesBio commented Dec 1, 2025

PR checklist

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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 ✅ ⚠️