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14 lines
533 B
Text
14 lines
533 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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params.save_mpileup = true
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include { IVAR_CONSENSUS } from '../../../../software/ivar/consensus/main.nf' addParams( [ options: [args2: '-aa -A -d 0 -Q 0'] ] )
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workflow test_ivar_consensus {
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def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
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def input = []
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input = [ [ id:'test'],
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file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
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IVAR_CONSENSUS ( input, ref )
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}
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