Config updates by DLBPointon · Pull Request #115 · sanger-tol/curationpretext

DLBPointon · 2025-09-16T11:31:41Z

Config Updates to match parity with TreeVal

Added an AUTO option for aligner, this way the pipeline will select minimap automatically if genome > 5Gb else bwamem2.

AUTO is now default for ease of use.

Comment out CONDA, pipeline doesn't support it anyway. Turned back on due to merge conflict.

…nd-user selection

github-actions · 2025-09-16T11:33:41Z

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

Posted for pipeline commit b921914

+| ✅ 194 tests passed       |+
#| ❔  32 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.5.0
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 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: 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 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.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: 24.10.5, Config: 24.10.5
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_comment.yml
actions_schema_validation - Workflow validation passed: fix_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: 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: clean-up.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: nf-test.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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-09-19 12:52:02

yumisims · 2025-09-16T14:57:58Z

should we discuss in the meeting whether should use auto? I think we should just default to minimap2, keep the option open for curators if they want to use bwamem2?

DLBPointon · 2025-09-19T10:25:04Z

@yumisims
I've confirmed with Jo that AUTO is fine to be left as the default. Some more in depth testing can be done later.

I'm just updating a couple of docs related things then this will be good to review.

prototaxites

LGTM!

DLBPointon added 3 commits September 16, 2025 12:28

Add switch for large genomes to switch over to MINIMAP2 rather than e…

bd428b3

…nd-user selection

Adding AUTO as option

512ac14

TreeVal Parity for the resource configs

d7e6c97

DLBPointon self-assigned this Sep 16, 2025

DLBPointon marked this pull request as ready for review September 16, 2025 11:31

DLBPointon added 4 commits September 16, 2025 12:36

Fat finger spelling mistake

0846295

Pipeline doesn't support conda

f799ad8

Update CHANGELOG

48f7b5c

remove conda this time

f39eecf

yumisims self-requested a review September 16, 2025 14:56

DLBPointon added 6 commits September 19, 2025 11:45

Update some text

dfa8f0b

add line on sample

39d021f

linting

be1c692

Update

8aa5341

Pre-commit linting

a74b9e1

Updates

b921914

prototaxites approved these changes Sep 22, 2025

View reviewed changes

DLBPointon merged commit 2f32cb3 into dev Sep 22, 2025
7 checks passed

DLBPointon deleted the config_updates branch October 3, 2025 11:06

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Config updates#115

Config updates#115
DLBPointon merged 13 commits intodevfrom
config_updates

DLBPointon commented Sep 16, 2025 •

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edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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yumisims commented Sep 16, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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yumisims commented Sep 16, 2025

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DLBPointon commented Sep 16, 2025 •

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