Add Metaphlan4 profiler #318

LilyAnderssonLee · 2023-07-07T07:38:49Z

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!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile 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).

github-actions · 2023-07-07T07:42:47Z

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

Posted for pipeline commit 1be2aaa

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

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

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
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files_exist - File found: conf/modules.config
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files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-taxprofiler_logo_light.png
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files_exist - File found: docs/output.md
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files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
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files_exist - File found: lib/WorkflowTaxprofiler.groovy
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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: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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 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 variable 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 ends in dev: 1.1.0dev
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
files_unchanged - .gitattributes matches the template
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files_unchanged - assets/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.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: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (191 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: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.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
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.9
Run at 2023-07-17 06:02:27

nextflow_schema.json

Midnighter

Changes look good to me. Amazing how many files had to be modified.

jfy133

I just remembered we couldn't support metaphlan in MultiQC.
Could you also remove it from the MultiQC section of output.md and also the multiqc_config.yml in the `run_modules section)
You will need to update the full_test database sheet on test-datasets to include teh --mpa3 parameter

CHANGELOG.md

docs/usage.md

jfy133 · 2023-07-20T11:29:41Z

docs/usage.md

@@ -731,21 +731,20 @@ You can then add the `<YOUR_DB_NAME>/` path to your nf-core/taxprofiler database
 <details markdown="1">
 <summary>Expected files in database directory</summary>


For MetaPhlAn4

subworkflows/local/db_check.nf

LilyAnderssonLee added 21 commits July 7, 2023 09:12

Add MetaPhlAn4 citation to CITATIONS.md

66800aa

Add MetaPhlAn4 to README.md

e10027b

Add profiler MetaPhlAn4 to modules.config

71dc963

Add profiler MetaPhlAn4 to conf/test.config

44df24f

Add profiler MetaPhlAn4 to conf/test_full.config

9ce1282

Add profiler MetaPhlAn4 to conf/test_krakenuniq.config

7537c0b

Add profiler MetaPhlAn4 to conf/test_motus.config

b212e94

Add profiler MetaPhlAn4 to conf/test_nopreprocessing.coconfig

b6b49b3

Add profiler MetaPhlAn4 to conf/test_noprofiling.config

15a4e1b

Add profiler MetaPhlAn4 to conf/test_nothing.config

708e81d

Add profiler MetaPhlAn4 to docs/images/taxprofiler_tube.svg

4fd9d55

Add MetaPhlAn4 to docs/output.md, docs/usage.md

fcf5166

Added parameters to nextflow.config

de4baeb

remove the module metaphlan3/metaphlan3

1706cc3

Remove the module metaphlan3/mergemetaphlantables

55d89f9

update the version of module taxpasta/merge, taxpasta/standardise

b21f113

Added profiler to expected tools in subworkflows/local/db_check.nf

d10e79d

Added profiler to subworkflows/local/profiling.nf

0b279c0

Added profiler to subworkflows/local/standardisation_profiles.nf

3b3a527

update the pipeline schema

61e4eca

install the module metaphlan

4531549

LilyAnderssonLee added 3 commits July 7, 2023 11:17

nf-core lint fix format .github/CONTRIBUTING.md

4f945e3

nf-core lint fix format

985464e

Update into the most recent version on dev

2f8e370

sofstam reviewed Jul 7, 2023

View reviewed changes

nextflow_schema.json Outdated Show resolved Hide resolved

LilyAnderssonLee and others added 4 commits July 10, 2023 11:36

Modify nextflow_schema.json

5cb7d97

comment krakenuniq step ci.yml

e03f317

Merge branch 'dev' into metaphlan4_profiler

d5d2bc3

Add MetaPhlAn4 to docs/usage.md

9b7ffb8

LilyAnderssonLee added 3 commits July 13, 2023 15:07

Add contribution to the CHANGELOG.md

9061278

uncomment KrakenUniq in ci.yml

75581b0

pull the ci.yml from dev branch

bc27e8a

LilyAnderssonLee requested a review from jfy133 July 14, 2023 14:47

Midnighter approved these changes Jul 14, 2023

View reviewed changes

LilyAnderssonLee added 2 commits July 17, 2023 07:59

Merge branch 'dev' into metaphlan4_profiler

14bed9d

Update CHANGELOG.md

1be2aaa

LilyAnderssonLee merged commit 36d3156 into nf-core:dev Jul 17, 2023

jfy133 reviewed Jul 20, 2023

View reviewed changes

LilyAnderssonLee self-assigned this Aug 10, 2023

LilyAnderssonLee added the enhancement Improvement for existing functionality label Aug 17, 2023

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Add Metaphlan4 profiler #318

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		@@ -731,21 +731,20 @@ You can then add the `<YOUR_DB_NAME>/` path to your nf-core/taxprofiler database
		<details markdown="1">
		<summary>Expected files in database directory</summary>

Add Metaphlan4 profiler #318

Add Metaphlan4 profiler #318

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nf-core lint overall result: Passed ✅ ⚠️

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