Add in container override by DarianHole · Pull Request #30 · phac-nml/measeq

DarianHole · 2026-02-06T22:05:21Z

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
Make sure your code lints (nf-core pipelines lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

Release 1.0.0

github-actions · 2026-02-06T22:05:31Z

This PR is against the `main` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

It looks like this pull-request is has been made against the phac-nml/measeq main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the phac-nml/measeq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2026-02-06T22:06:30Z

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

Posted for pipeline commit 213c3a1

+| ✅ 165 tests passed       |+
#| ❔  48 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
nextflow_config - Config manifest.version should end in dev: 1.0.1
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred 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!

❔ Tests ignored:

files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File is ignored: .github/CONTRIBUTING.md
files_exist - File is ignored: .github/.dockstore.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: assets/email_template.txt
files_exist - File is ignored: assets/email_template.html
files_exist - File is ignored: assets/sendmail_template.txt
files_exist - File is ignored: assets/adaptivecard.json
files_exist - File is ignored: assets/slackreport.json
files_exist - File is ignored: assets/nf-core-measeq_logo_light.png
files_exist - File is ignored: docs/images/nf-core-measeq_logo_light.png
files_exist - File is ignored: docs/images/nf-core-measeq_logo_dark.png
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: CODE_OF_CONDUCT.md
files_exist - File is ignored: ro-crate-metadata.json
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: process.cpus
nextflow_config - Config variable ignored: process.memory
nextflow_config - Config variable ignored: process.time
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 does not exist: .github/.dockstore.yml
files_unchanged - File does not exist: .github/CONTRIBUTING.md
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File does not exist: .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 does not exist: assets/email_template.html
files_unchanged - File does not exist: assets/email_template.txt
files_unchanged - File does not exist: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-measeq_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-measeq_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-measeq_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/measeq/measeq/.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: .editorconfig
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/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: conf/modules.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: main.nf
files_exist - File found: conf/base.config
files_exist - File found: modules.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-measeq_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/WorkflowMeaseq.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-validation 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: 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 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 - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.ivar_trim_min_read_length= 30
nextflow_config - Config default value correct: params.min_ambiguity_threshold= 0.3
nextflow_config - Config default value correct: params.max_ambiguity_threshold= 0.75
nextflow_config - Config default value correct: params.min_indel_threshold= 0.6
nextflow_config - Config default value correct: params.min_alt_fraction_freeabyes= 0.05
nextflow_config - Config default value correct: params.min_variant_qual_freebayes= 20
nextflow_config - Config default value correct: params.ont_min_read_length= 200
nextflow_config - Config default value correct: params.ont_min_base_qual= 12
nextflow_config - Config default value correct: params.normalise_ont= 500
nextflow_config - Config default value correct: params.ont_keep_incorrect_primers= false
nextflow_config - Config default value correct: params.min_variant_qual_c3= 7
nextflow_config - Config default value correct: params.min_depth= 10
nextflow_config - Config default value correct: params.neg_control_pct_threshold= 10
nextflow_config - Config default value correct: params.neg_ctrl_substrings= neg,ntc,blank,en
nextflow_config - Config default value correct: params.nextclade_dataset_name= nextstrain/measles/N450/WHO-2012
nextflow_config - Config default value correct: params.nextclade_dataset_tag= 2025-03-26--11-47-13Z
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Zenodo placeholder was replaced with DOI.
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: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci_workflow.yml
actions_schema_validation - Workflow validation passed: branch.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.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - NANOQ found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - BWAMEM2_MEM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_CONSENSUS_AMBIGUOUS found in conf/modules.config and Nextflow scripts.
modules_config - NEXTCLADE_DATASETGET found in conf/modules.config and Nextflow scripts.
modules_config - NEXTCLADE_RUN_N450 found in conf/modules.config and Nextflow scripts.
modules_config - NEXTCLADE_RUN_CUSTOM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_COVERAGE found in conf/modules.config and Nextflow scripts.
modules_config - QUAST found in conf/modules.config and Nextflow scripts.
modules_config - CALCULATE_BAM_VARIATION found in conf/modules.config and Nextflow scripts.
modules_config - STAGE_FILE_IRIDANEXT found in conf/modules.config and Nextflow scripts.
modules_config - GENERATE_REF_INTERMEDIATES found in conf/modules.config and Nextflow scripts.
modules_config - GENERATE_AMPLICON_BED found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_AMPLICON_REGION found in conf/modules.config and Nextflow scripts.
modules_config - PREDICT_GENOTYPE found in conf/modules.config and Nextflow scripts.
modules_config - BWAMEM2_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - IVAR_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - FREEBAYES found in conf/modules.config and Nextflow scripts.
modules_config - PROCESS_VCF found in conf/modules.config and Nextflow scripts.
modules_config - ARTIC_GET_MODELS found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - ARTIC_ALIGN_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - CLAIR3 found in conf/modules.config and Nextflow scripts.
modules_config - ARTIC_VCF_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_VCF_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_NORM found in conf/modules.config and Nextflow scripts.
modules_config - VCF_TO_TSV found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_CONSENSUS found in conf/modules.config and Nextflow scripts.
modules_config - ADJUST found in conf/modules.config and Nextflow scripts.
modules_config - COMPARE_INTERNAL_DSID found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_SAMPLE_QC_CSV found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_FINAL_QC_CSV found in conf/modules.config and Nextflow scripts.
modules_config - SAMPLE_AMPLICON found in conf/modules.config and Nextflow scripts.
modules_config - AMPLICON_ found in conf/modules.config and Nextflow scripts.
modules_config - AMPLICON_MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - POSITIONAL_N_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - PYSAMSTATS found in conf/modules.config and Nextflow scripts.
modules_config - NORMALIZE_DEPTH_MATRIX found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_CUSTOM_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 3.2.1

Run details

nf-core/tools version 3.2.1
Run at 2026-02-09 14:48:25

apetkau

This looks really good. Only some minor comments.

apetkau · 2026-02-09T14:35:39Z

+        container = {
+            workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+                ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/88/889a182b8066804f4799f3808a5813ad601381a8a0e3baa4ab8d73e739b97001/data'
+                : !task.ext.override_configured_container_registry


Could you change to task.ext.override_configured_container_registry != false instead? That way, this check works even if task.ext.override_configured_container_registry is unset or null.

DarianHole and others added 3 commits February 4, 2026 14:39

Merge pull request #28 from phac-nml/dev

30e15d0

Release 1.0.0

Fix errant missed README link

42bdd00

adjust report label, add in container override

5a21008

DarianHole changed the base branch from main to dev February 6, 2026 22:05

update changelog and version numbers

c094eb2

apetkau approved these changes Feb 9, 2026

View reviewed changes

Adjust override_configured_container_registry to use != false

213c3a1

DarianHole merged commit ef32f55 into dev Feb 9, 2026
8 checks passed

DarianHole deleted the update/containers branch February 9, 2026 15:23

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Add in container override#30

Add in container override#30
DarianHole merged 5 commits into
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update/containers

DarianHole commented Feb 6, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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DarianHole commented Feb 6, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR checklist

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github-actions Bot commented Feb 6, 2026

This PR is against the main branch ❌

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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DarianHole commented Feb 6, 2026 •

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This PR is against the `main` branch ❌

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