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41 lines
1.6 KiB
Text
41 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
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params.gff = false
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params.save_mpileup = false
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workflow test_ivar_variants_no_gff_no_mpileup {
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def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
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def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
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def input = []
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input = [ [ id:'test'],
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file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
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IVAR_VARIANTS ( input, ref, dummy )
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}
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params.gff = false
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params.save_mpileup = true
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workflow test_ivar_variants_no_gff_with_mpileup {
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def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
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def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
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def input = []
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input = [ [ id:'test'],
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file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
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IVAR_VARIANTS ( input, ref, dummy )
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}
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params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
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workflow test_ivar_variants_with_gff_with_mpileup {
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def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
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def gff = file(params.gff, 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_VARIANTS ( input, ref, gff )
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}
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