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Sketch test for kraken subworkflow
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Aratz committed Oct 18, 2023
1 parent 6644e59 commit cfaa725
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39 changes: 39 additions & 0 deletions tests/pipeline/kraken.nf.test
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nextflow_workflow {

name "Test Workflow "
script "workflows/demultiplex.nf"
workflow "DEMULTIPLEX"
tag "kraken"
tag "pipeline"

test("KRAKEN") {

setup {
run("UNTAR") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = Channel.of([ [], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/db/kraken2.tar.gz", checkIfExists: true) ])
"""
}
}
}

when {
params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
demultiplexer = 'bclconvert'
outdir = "$outputDir"
//kraken_db = UNTAR.out.untar.map{ it[1] }
}
}

then {
assertAll(
{ assert workflow.success },
)
}

}

}

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