Strict syntax by weaglesBio · Pull Request #455 · sanger-tol/treeval

weaglesBio · 2026-02-13T17:00:43Z

PR checklist

Strict Syntax and update to modules

sanger-tolsoft · 2026-02-13T17:01:17Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

github-actions · 2026-02-13T17:02:46Z

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

Posted for pipeline commit 357cfee

+| ✅ 218 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 115]
system_exit - System.exit in treeval.nf: System.exit(1) [line 122]

❔ 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 - 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 - JUICERTOOLS_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 - 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_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 - 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 2026-02-20 13:13:25

DLBPointon

Still looking for the task error bit, but some stuff I saw on the way through.

subworkflows/local/gap_finder/main.nf

subworkflows/local/generate_sorted_genome/main.nf

subworkflows/local/generate_unsorted_genome/main.nf

subworkflows/local/selfcomp/main.nf

subworkflows/local/synteny/main.nf

DLBPointon · 2026-02-18T11:31:34Z

subworkflows/local/yaml_input/main.nf

@@ -111,7 +108,7 @@ def readYAML(yamlfile) {
    return new org.yaml.snakeyaml.Yaml().load(new FileReader(yamlfile.toString()))
 }

-def fn_get_validated_channel (data_type, tolid_ver, read_type, defined_class, project_id, files_list) {
+def fn_get_validated_channel (data_type, tolid_ver, read_type, _defined_class, _project_id, files_list) {


Worth moving the functions to a new place? functions/local/utils.nf and import

weaglesBio added 4 commits February 10, 2026 17:22

Initial fixes

ed91f7c

Strict syntax update

d4d425c

Start modules update

d82ecda

Update modules

88f1aa6

weaglesBio added 7 commits February 16, 2026 16:12

Fix module params

ab3a906

Remove unused module

2de30c3

Replace juicer module

10181a8

Update minimap2/align

012fa0c

Remove versions reference

d327b1c

Lint fix

a1edb8b

Remove log

ccb689d

weaglesBio marked this pull request as ready for review February 17, 2026 15:49

weaglesBio requested review from DLBPointon and yumisims February 17, 2026 15:50

DLBPointon reviewed Feb 18, 2026

View reviewed changes

DLBPointon and others added 10 commits February 18, 2026 12:07

Fix issue with renameTo -> moveTo

a837e6a

Input tuple fix

1a6dd10

Change ifEmpty(channel) to ifEmpty([])

e445d99

Fix Versions channel, also a ch_versions override which we didn't notice

0564a04

Remove version channels where no longer needed

513feb1

Fix versions out

b621718

Minor changes

93d2e1c

Testing fixes

064f838

Remove renaming

38cdde5

Update test

357cfee

DLBPointon approved these changes Feb 20, 2026

View reviewed changes

DLBPointon merged commit 3751dd5 into dev Feb 20, 2026
7 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Strict syntax#455

Strict syntax#455
DLBPointon merged 21 commits intodevfrom
strict_syntax

weaglesBio commented Feb 13, 2026

Uh oh!

sanger-tolsoft commented Feb 13, 2026

Uh oh!

github-actions bot commented Feb 13, 2026 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

DLBPointon left a comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

DLBPointon Feb 18, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Conversation

weaglesBio commented Feb 13, 2026

PR checklist

Uh oh!

sanger-tolsoft commented Feb 13, 2026

Uh oh!

github-actions bot commented Feb 13, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

DLBPointon left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

DLBPointon Feb 18, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

github-actions bot commented Feb 13, 2026 •

edited

Loading

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