Move import in utils_nfcore_phaseimpute_pipeline

[LouisLeNezet]

PR checklist

This PR should remove warning in nf-core pipelines lint for the different import use in the email workflow.

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[LouisLeNezet]

Is it good now @mashehu ?

[mirpedrol]

Hello @LouisLeNezet, when do you see this warning? and could you explain why is this change solving it? Thanks!

[LouisLeNezet]

Hi,

Here is the warning that I can get by running nf-core pipelines lint on the TEMPLATE branch of phaseimpute.

╭─ [!] 16 Subworkflow Test Warnings ────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                    ╷                                                      ╷                                                       │
│ Subworkflow name                   │ File path                                            │ Test message                                          │
│╶───────────────────────────────────┼──────────────────────────────────────────────────────┼──────────────────────────────────────────────────────╴│
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'completionEmail' not used in      │
│                                    │                                                      │ main.nf                                               │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'completionSummary' not used in    │
│                                    │                                                      │ main.nf                                               │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'imNotification' not used in       │
│                                    │                                                      │ main.nf                                               │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'paramsSummaryMap' not used in     │
│                                    │                                                      │ main.nf                                               │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'UTILS_NEXTFLOW_PIPELINE' versions │
│                                    │                                                      │ are not added in main.nf                              │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'UTILS_NFCORE_PIPELINE' versions   │
│                                    │                                                      │ are not added in main.nf                              │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'UTILS_NFSCHEMA_PLUGIN' versions   │
│                                    │                                                      │ are not added in main.nf                              │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'completionEmail' versions are not │
│                                    │                                                      │ added in main.nf                                      │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'completionSummary' versions are   │
│                                    │                                                      │ not added in main.nf                                  │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'imNotification' versions are not  │
│                                    │                                                      │ added in main.nf                                      │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'paramsSummaryMap' versions are    │
│                                    │                                                      │ not added in main.nf                                  │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Included component 'samplesheetToList' versions are   │
│                                    │                                                      │ not added in main.nf                                  │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ Subworkflow meta.yml does not exist                   │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ TODO string in main.nf: Only uncomment below if logic │
│                                    │                                                      │ in toolCitationText/toolBibliographyText has been     │
│                                    │                                                      │ filled!                                               │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ TODO string in main.nf: Optionally add bibliographic  │
│                                    │                                                      │ entries to this list.                                 │
│ utils_nfcore_phaseimpute_pipeline  │ subworkflows/local/utils_nfcore_phaseimpute_pipelin… │ TODO string in main.nf: Optionally add in-text        │
│                                    │                                                      │ citation tools to this list.                          │
│                                    ╵                                                      ╵                                                       │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

I don't really know how this linting is done but just by moving the import above the concerned workflow solved the issue. So we might either keep the importation near the workflow or change the linting to check the import for all workflow scope in the main.nf.

[mirpedrol]

I can see the warning in phaseimpute but not in other pipelines, so the error must be somewhere else, the location of imports should always be at the top of the file

[LouisLeNezet]

The other issue is that in many pipelines the linting of subworkflows is deactivated as they've added lines in the .nf-core.yml

[mirpedrol]

Found the error. This line should be
if lint_obj.lint_config and lint_obj.lint_config["nfcore_components"] is not None:, because we set all lint_config fields to None by default

[mirpedrol]

This local subworkflow is a bit different because we have several workflows, usually we only have 1 workflow per subworkflow. I would modify the main_nf() function, it should take into account all the workflows when checking the included components

[LouisLeNezet]

Okay so I will close this PR. Should I open a new issue regarding the default linting and the main.nf() ?

[mirpedrol]

That would be great, thanks!