Fix incorrect references to RAPID-TOL by DLBPointon · Pull Request #472 · sanger-tol/treeval

DLBPointon · 2026-05-13T10:42:21Z

Fixes related to #471

Fixes to usage.md where RAPID_TOL was incorrectly down as RAPID-TOL
Over zealous required values in the schema, stopping people from just not adding things like kmer_profile information to the input file.
Due to the above, YAML_INPUT was not treating null values correctly
- Fixes started with kmer_profile data.

sanger-tolsoft · 2026-05-13T10:43:00Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
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 · 2026-05-13T10:45:27Z

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

Posted for pipeline commit d354740

+| ✅ 220 tests passed       |+
#| ❔  30 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  10 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.4.7
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 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 methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
system_exit - System.exit in treeval.nf: System.exit(1) [line 113]
system_exit - System.exit in treeval.nf: System.exit(1) [line 120]

❔ 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: .gitattributes
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 fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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.kmer_length= 31
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 - .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: template-version-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 - PRETEXTMAP_ULTRA 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 - TABIX_BGZIPTABIX 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_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 - PRETEXTMAP_ULTRA 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 - PRETEXT_INGEST_ULTRA 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: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-06-09 16:32:25

DLBPointon · 2026-05-13T12:36:36Z

We would be able to have much better control of the required data per mode if params.mode were to move into the yaml rather than the cli.

…er length

muffato

(I know this PR is only about documenting the actual process, so this is not in scope of this PR. Something else to consider). I think the BED etc files should be compressed as they can be quite big otherwise. I understand that the "big" versions are binary and less practical to use, but a bgzip is already quite good

nikostr · 2026-05-20T08:40:59Z

Would it make sense to get rid of the 'punchlist' nomenclature as a part of this PR, and replace that word with short descriptions of what the files contain?

DLBPointon · 2026-06-09T15:41:11Z

Would it make sense to get rid of the 'punchlist' nomenclature as a part of this PR, and replace that word with short descriptions of what the files contain?

Apologies for the wait, other projects had to take precedence. We won't be able to get rid of the term straight away, unfortunately they are used in some strict file/directory matching in downstream processes. We will make and effort to making it more generic in the future though, for now I've added a quick explainer to the docs.

muffato

Some minor comments. Nothing blocking

Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr> Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>

Fix incorrect references to RAPID-TOL

c0efbe0

DLBPointon self-assigned this May 13, 2026

DLBPointon added this to WRAP team board May 13, 2026

github-project-automation Bot moved this to Todo in WRAP team board May 13, 2026

DLBPointon moved this from Todo to In progress in WRAP team board May 13, 2026

DLBPointon marked this pull request as draft May 13, 2026 10:42

DLBPointon mentioned this pull request May 13, 2026

Usage yaml documentation outdated #471

Open

DLBPointon added 4 commits May 13, 2026 14:54

Previous links were pointing to deleted files, update to existing ones

7e7adae

Update to remove too many required data

5ecff83

Update to move kmer_profile data into empty channel if not provided

c72ddd5

Add note, that subworkflows will only run if their data is in the yaml

53a2c28

DLBPointon mentioned this pull request May 13, 2026

docs: fix outdated YAML example links #473

Closed

DLBPointon added 8 commits May 13, 2026 17:42

Update to remove kmer_profile yaml args and replace with a cli for km…

f28ad52

…er length

Update more

c8c4f45

Update documentation

589d4ed

Update to nullify busco if not found

98106b0

Update docs

318dee7

Update the local testing yamls

e3b3abb

Add proposal for v2 of treeval input

21a30d4

Update to remove fields no longer needed

a7a299e

DLBPointon marked this pull request as ready for review May 19, 2026 09:25

muffato reviewed May 19, 2026

View reviewed changes

Comment thread CHANGELOG.md

Comment thread assets/local_testing/params.json

DLBPointon mentioned this pull request Jun 9, 2026

Review suitability of gzipping bed files #476

Open

Add clarification on punchlists

cf2d40f

DLBPointon requested a review from muffato June 9, 2026 15:41

muffato approved these changes Jun 9, 2026

View reviewed changes

Comment thread assets/treeval_v2_input_proposal/samplesheet.csv

Comment thread assets/local_testing/params.json

Comment thread assets/treeval_v2_input_proposal/production.config Outdated

DLBPointon commented Jun 9, 2026

View reviewed changes

Comment thread assets/treeval_v2_input_proposal/samplesheet.csv Outdated

Apply suggestions from code review

d354740

Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr> Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>

DLBPointon merged commit 12a423b into dev Jun 9, 2026
7 checks passed

github-project-automation Bot moved this from In progress to Done in WRAP team board Jun 9, 2026

DLBPointon deleted the 471-fixes branch June 9, 2026 17:59

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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