Dev by kathrynmurie · Pull Request #90 · nf-core/plasmodiumdrugres

kathrynmurie · 2026-08-14T21:34:09Z

Merging into main to do first release of pipeline

PR checklist

…tions add instructions about cloning the repo

… platform from nextflow config

…w_note Hotfix/add temporary nextflow note

…m_and_instructions add instructions for pulling image with different platform and remove…

Hotfix/docker failing build

Update colours, tools, and structure of metro map

…with population names with spaces and special characters

…uts and all columns from tools

Stop tracking .vscode and ignore i

index population assignment and use this internally to remove issues …

… into config; fix Channel to channel

…ate how methods are validated

…me in concat

…d_outputs Update tool option handling and add subworkflow meta files

…for raw_smmaries output

…any required column is missing

Standardise outputs from tools

allow no loci groups and ml won't run

…fig so linting passes

…rs_and_flow Accurately represent current state in metromap; Update colours

Hotfix/update env documentation

bump pipeline version for release and update snapshots

github-actions · 2026-08-14T21:35:21Z

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

Posted for pipeline commit 076642a

+| ✅ 205 tests passed       |+
#| ❔   6 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   4 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in CHANGELOG.md: ## v1.0.0dev - [unreleased replace with date on release ]
pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_unchanged - File ignored due to lint config: assets/nf-core-plasmodiumdrugres_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-plasmodiumdrugres_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-plasmodiumdrugres_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
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: CODE_OF_CONDUCT.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/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.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/pr-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: assets/nf-core-plasmodiumdrugres_logo_light.png
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/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-plasmodiumdrugres_logo_light.png
files_exist - File found: docs/images/nf-core-plasmodiumdrugres_logo_dark.png
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: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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-plasmodiumdrugres_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/WorkflowPlasmodiumdrugres.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.name
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: manifest.homePage
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 manifest.name began with nf-core/
nextflow_config - Config manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 1.0.0
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.pmo_population_separator= _
nextflow_config - Config default value correct: params.outdir= output
nextflow_config - Config default value correct: params.mlaf_method= naive
nextflow_config - Config default value correct: params.slaf_method= naive
nextflow_config - Config default value correct: params.naive_slaf_method= read_count_prop
nextflow_config - Config default value correct: params.population_label= pop1
nextflow_config - Config default value correct: params.naive_mlaf_method= wsaf_prop
nextflow_config - Config default value correct: params.slaf_method_mhaps_freq_method= dcifer
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/refs/heads/plasmodiumdrugres/
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/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' 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 - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/pr-comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md 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
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
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: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: nf-test.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 - TRANSLATE_LOCI_OF_INTEREST found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_TABLES 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: 4.1.0
rocrate_readme_sync - RO-Crate description matches the README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date
version_consistency - Version tags are consistent: manifest.version = 1.0.0, nfcore_yml.version = 1.0.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 4.1.0
Run at 2026-08-14 21:35:03

kathrynmurie and others added 30 commits April 21, 2026 06:51

add instructions about cloning the repo

d9efc5f

Merge pull request #60 from PlasmoGenEpi/feature/add_clone_to_instruc…

0cf24d2

…tions add instructions about cloning the repo

add instructions for pulling image with different platform and remove…

fb70452

… platform from nextflow config

run pre-commit

b3ff51c

correct docker tag

e1b7afa

add note about not supporting nextflow 26

99d3b31

update linting

592a427

Merge pull request #66 from PlasmoGenEpi/hotfix/add_temporary_nextflo…

60b7a80

…w_note Hotfix/add temporary nextflow note

Update colours, tools, and structure of metro map

b12d47f

revert platform

a9a1db6

pegas no lon(base) kmurie@UC03-525-10678 bin % git status

177566f

update nmle build for pegas and ape

a3b4ef6

pin nextflow version for tests

d6321bd

Merge pull request #65 from PlasmoGenEpi/hotfix/update_docker_platfor…

bc37704

…m_and_instructions add instructions for pulling image with different platform and remove…

Merge pull request #71 from PlasmoGenEpi/hotfix/docker_failing_build

87484bb

Hotfix/docker failing build

Merge pull request #70 from PlasmoGenEpi/hotfix/update_metro_maps

47cf07c

Update colours, tools, and structure of metro map

index population assignment and use this internally to remove issues …

b6073db

…with population names with spaces and special characters

Stop tracking .vscode and ignore i

6867c15

Standardise outputs from tools and add raw folder with secondary outp…

248a8d5

…uts and all columns from tools

Install pmotools correctly

07d510f

update dockerfile to install versioned pmotools

f99bed1

fix pre-commit

c13d581

Merge pull request #74 from PlasmoGenEpi/hotfix/remove_vscode

7e626d1

Stop tracking .vscode and ignore i

Merge branch 'dev' into feature/remove_popID_dependency

853c365

check and update split allele table test

60cff51

Merge pull request #73 from PlasmoGenEpi/feature/remove_popID_dependency

f66e5d7

index population assignment and use this internally to remove issues …

Merge branch 'dev' into feature/add_loci_info_to_slaf

01a10eb

fix pre-commit

4bab097

check and update snapshot

f5217cf

update linting param intput

37e938e

kathrynmurie added 29 commits August 7, 2026 11:54

fix defaults in docs and clean output.md; remove hardcoded publishDir…

60c6f40

… into config; fix Channel to channel

Add meta files to subworkflows; Remove nf-core test data comment; Upd…

34a706a

…ate how methods are validated

resolve merge conflicts

dcc9322

Make empty ml table explicit in the documentation and use full filena…

930fea4

…me in concat

Fix tests

d976d87

Update for strict syntax

32e4acd

Merge pull request #85 from PlasmoGenEpi/hotfix/small_updates_docs_an…

a5f105c

…d_outputs Update tool option handling and add subworkflow meta files

Merge branch 'dev' into feature/allow_no_ml_run

7cec3e0

update snapshot for testing without mlaf

f2c16be

Resolve merge conflicts; update documentation; remove redundant line …

14e2457

…for raw_smmaries output

update concat module

cf9b091

Update column check in concat tables for ml_summary, to fail once if …

ff2d5f2

…any required column is missing

Remove unnesserary comments

71e0bc9

Merge pull request #75 from PlasmoGenEpi/feature/add_loci_info_to_slaf

7886fcc

Standardise outputs from tools

Merge dev and resolve merge conflict

9a6e551

Update for failures caused by empty ml_summary

e2c2cea

Merge pull request #78 from PlasmoGenEpi/feature/allow_no_ml_run

31b1e28

allow no loci groups and ml won't run

bump pipeline version for release and update snapshots

734e815

Added config stub for pipeline to nf-core repo. Uncommenting this con…

1cbef57

…fig so linting passes

Accurately represent current state in metromap. Update colours

3c40f36

Update environment instructions

b779260

update slaf methods

a1c47e7

remove unnecessary detail from README that should be in usage

7c704a7

update PMO population param explanation

0bf8689

corrrecting usage docs

ecdfdca

Merge pull request #88 from PlasmoGenEpi/hotfix/update_metromap_colou…

8475030

…rs_and_flow Accurately represent current state in metromap; Update colours

Merge pull request #89 from PlasmoGenEpi/hotfix/update_env_documentation

21aa1a6

Hotfix/update env documentation

Merge branch 'dev' into feature/prepare_release

531c404

Merge pull request #86 from PlasmoGenEpi/feature/prepare_release

076642a

bump pipeline version for release and update snapshots

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kathrynmurie commented Aug 14, 2026 •

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github-actions Bot commented Aug 14, 2026

❗ Test warnings:

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github-actions Bot commented Aug 14, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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kathrynmurie commented Aug 14, 2026 •

edited

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