Fix multiple workflow in subworkflow

[LouisLeNezet]

PR checklist

This PR should close #3479
However when multiple workflow are present in one main.nf the input and output are aggregated for all. Therefore if one of the workflow does not have any input or output but the other one does, no error will be thrown.
An easy fix would be to ban any file with more than one workflow (need template modification for local/utils_nfcore_*_pipeline

• 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

[codecov]

Codecov Report

Attention: Patch coverage is 85.71429% with 2 lines in your changes missing coverage. Please review.

Project coverage is 76.93%. Comparing base (5b1d830) to head (8dcb1c5).

Files with missing lines	Patch %	Lines
nf_core/subworkflows/lint/main_nf.py	85.71%	2 Missing ⚠️

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[LouisLeNezet]

After consideration, I think it would be better to not allow the presence of mutliple process / workflow in a single file.
Doing so would allow for a better description (one meta.yml / workflow) and organisation (simpler nf-test).
What do you think ?

[mirpedrol]

After consideration, I think it would be better to not allow the presence of mutliple process / workflow in a single file.
Doing so would allow for a better description (one meta.yml / workflow) and organisation (simpler nf-test).
What do you think ?

I agree with this @LouisLeNezet 👍

[LouisLeNezet]

Hi,
I've tried locally to reproduce the error, but it might be linked to the latest nextflow version.

N E X T F L O W  ~  version 25.02.0-edge
Launching `my-prefix-testpipeline/main.nf` [sharp_snyder] DSL2 - revision: 2017146e03
Downloading plugin [email protected]
A workflow named 'UTILS_NFSCHEMA_PLUGIN' is already defined or included in script: /home/runner/work/tools/tools/create-test-lint-wf/my-prefix-testpipeline/subworkflows/local/utils_nfcore_testpipeline_pipeline/main.nf

[mirpedrol]

the samplesheet can be csv, tsv, yamls or json

[LouisLeNezet]

Yeah but this is the output of the read samplesheet.
In the template it only contains the metamap and fastq files, no ?