Hi, I've fully migrated nf-core/phaseimpute to topic usage. I'm however confronted to

nf_test_content: 'tests/default.nf.test' does not snapshot a 'versions.yml' file

. The issue being that I do not have anymore such a file. Here is my test

then {
    assertAll(
        { assert workflow.success },
        { assert snapshot(
            UTILS.getPipelineResults(outputDir, workflow),
            [
                "all_samples.glimpse1": UTILS.vcfDetails("$outputDir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz")
            ]
        ).match() }
    )
}

With

UTILS.getPipelineResults

class UTILS {
    public static def getPipelineResults(outdir, workflow){
        return [
            "workflow size": workflow.trace.succeeded().size(),
            "versions" : removeNextflowVersion("$outdir/pipeline_info/nf_core_phaseimpute_software_mqc_versions.yml"),
            ...
        ]
    }
}

The pipeline should still create that file with topics 😛

#C01NHS4CC91 is fully migrated and create such a file

What I don't get is that I do have

"pipeline_info/nf_core_phaseimpute_software_mqc_versions.yml"

in my snapshot, but I still get the error 😕

@mashehu any ideas?

After a bit of debugging, the might come from the fact that I store all the results in a dictionnary and not a list.

How do you get a dictionnary?

It's was just because I used

return [
            "workflow size": workflow.trace.succeeded().size(),
            "versions" : removeNextflowVersion("$outdir/pipeline_info/nf_core_phaseimpute_software_mqc_versions.yml"),
            ...
        ]

Oh I see

After reading a bit more carefully, it's the

.nf.test

that needs to contains

versions.yml

. As I'm using a wrapper this is not detected. However if I change my

default.nf.test

to the following, i don't get the error anymore.

nextflow_pipeline {

    name "Test pipeline"
    script "../main.nf"
    tag "pipeline"
    tag "nf-core/phaseimpute"
    tag "test"

    test("-profile test") {
        config "../conf/test.config"
        when {
            params {
                publish_dir_mode = "copy"
                pipelines_testdata_base_path = '<https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/>'
                outdir = "$outputDir"
            }
        }

        then {
            assertAll(
                { assert workflow.success },
                { assert snapshot(
                    versions.yml, // With this line no more errors !
                    UTILS.getPipelineResults(outputDir, workflow),
                    [
                        "all_samples.glimpse1": UTILS.vcfDetails("$outputDir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz")
                    ]
                ).match() }
            )
        }

    }
}

I wrote a check in nf-test so that anything not written by me will fail

God damnit ! It's the same for seqinspector and sarek. You don't have a

versions.yml

in the default.nf.test but you don't have the error...

-> https://github.com/nf-core/seqinspector/blob/master/.nf-core.yml#L13

Seriously !! This is cheating

You're French, you should know there are rules and rules

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