Update for v25.11.0-edge

[DLBPointon]

Bunch of updates to get the pipeline running for 25.11.0-edge

Major edits include:

• test data to be downloaded curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf -
• test profile doesn't seem to be getting used correctly? Just using test profile results in a params parsing error for input and cram. So need to use absolute paths for them on CI

./nextflow-25.11.0-edge-dist run main.nf -profile test,docker --input /Users/dp24/Documents/curationpretext/TreeValTinyData/assembly/draft/grTriPseu1.fa --cram /Users/dp24/Documents/curationpretext/TreeValTinyData/genomic_data/hic-arima/

ERRORS

02/12/2025

(nextflow-edge) dp24@mib119764s:[Documents/curationpretext] (attempt_4):$: ./nextflow-25.11.0-edge-dist run main.nf -profile test,docker --input /Users/dp24/Documents/curationpretext/TreeValTinyData/assembly/draft/grTriPseu1.fa --cram /Users/dp24/Documents/curationpretext/TreeValTinyData/genomic_data/hic-arima/

 N E X T F L O W   ~  version 25.11.0-edge

Launching `main.nf` [peaceful_swanson] DSL2 - revision: c53b683c53

WARN: Unrecognized config option 'trace.override'
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
WARN: Unrecognized config option 'validation.help.enabled'
WARN: Unrecognized config option 'validation.help.command'
WARN: Unrecognized config option 'validation.help.fullParameter'
WARN: Unrecognized config option 'validation.help.showHiddenParameter'
Input/output options
  input              : /Users/dp24/Documents/curationpretext/TreeValTinyData/assembly/draft/grTriPseu1.fa
  skip_tracks        : NONE
  read_type          : hifi
  cram               : /Users/dp24/Documents/curationpretext/TreeValTinyData/genomic_data/hic-arima/
  teloseq            : TTAGGG
  map_order          : unsorted
  aligner            : AUTO
  run_hires          : true
  outdir             : pretext_rerun_CPRETEXT_OUTPUT
  sample             : pretext_rerun

Generic options
  tracedir           : pretext_rerun_CPRETEXT_OUTPUT/pipeline_info
  trace_report_suffix: 2025-12-02_10-58-09

Core Nextflow options
  runName            : peaceful_swanson
  containerEngine    : docker
  launchDir          : /Users/dp24/Documents/curationpretext
  workDir            : /Users/dp24/Documents/curationpretext/work
  projectDir         : /Users/dp24/Documents/curationpretext
  userName           : dp24
  profile            : test,docker
  configFiles        : /Users/dp24/Documents/curationpretext/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
Missing `fromPath` parameter

This immediately kills the pipeline, with the .nextflow.log not containing any more details than:

02_12_25_nextflow.log

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fb314b8

+| ✅ 191 tests passed       |+
#| ❔  32 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 1.5.1
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
• schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: assets/multiqc_config.yml
• files_exist - File is ignored: assets/nf-core-curationpretext_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_dark.png
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• 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 does not exist: 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/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.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_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/email_template.html
• 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 does not exist: assets/nf-core-curationpretext_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-curationpretext_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/curationpretext/curationpretext/.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: conf/test_full.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-curationpretext_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/WorkflowCurationpretext.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.all_output= false
• nextflow_config - Config default value correct: params.multi_mapping= 0.0
• 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/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
• 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.
• readme - README Zenodo placeholder was replaced with DOI.
• 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_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• 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: sanger_test.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 - 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 - PRETEXT_GRAPH 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 - SNAPSHOT_SRES 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 - GAP_LENGTH found in conf/base.config and Nextflow scripts.
• base_config - CRAM_GENERATE_CSV found in conf/base.config and Nextflow scripts.
• base_config - GNU_SORT found in conf/base.config and Nextflow scripts.
• base_config - BEDTOOLS_INTERSECT found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - PRETEXT_INGEST_SNDRD found in conf/modules.config and Nextflow scripts.
• modules_config - SNAPSHOT_SRES found in conf/modules.config and Nextflow scripts.
• modules_config - PRETEXTMAP_HIGHRES found in conf/modules.config and Nextflow scripts.
• modules_config - UCSC_BEDGRAPHTOBIGWIG 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_GAP_LENGTH found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_GENERATE_GENOME_FILE found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_UPPER_SEQUENCE found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_SPLIT_DIRECTIONS 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 - 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 - SNAPSHOT_SRES found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_INDEX 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 - PRETEXTMAP_STANDRD found in conf/modules.config and Nextflow scripts.
• modules_config - PRETEXTMAP_HIGHRES 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 description matches the README.md.

Run details

• nf-core/tools version 3.5.1
• Run at 2026-02-06 20:03:30

[bentsherman]

Regarding the config warnings:

• trace.override should be trace.overwrite -- finally a true positive, though still hard to see among all the false positive warnings 😅

• the validation config options are from the nf-schema plugin which was recently added linter / language server support for the validation config scope. I think you have to use 2.5.0 or newer

[sanger-tolsoft]

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.