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30 lines
No EOL
1.1 KiB
Text
30 lines
No EOL
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { TIDDIT_SV } from '../../../../software/tiddit/sv/main.nf' addParams( options: [:] )
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include { SAMTOOLS_FAIDX } from '../../../../software/samtools/faidx/main.nf' addParams( options: [:] )
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workflow test_tiddit_sv {
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def input = []
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def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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input = [ [ id:'test' ], // meta map
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[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
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SAMTOOLS_FAIDX ( fasta )
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TIDDIT_SV ( input, fasta, SAMTOOLS_FAIDX.out.fai )
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}
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workflow test_tiddit_sv_no_ref {
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def input = []
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def dummy_file = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
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def dummy_file2 = file("${launchDir}/tests/data/dummy/dummy_file2.txt", checkIfExists: true)
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input = [ [ id:'test' ], // meta map
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[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
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TIDDIT_SV ( input, dummy_file, dummy_file2 )
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} |