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https://github.com/MillironX/nf-core_modules.git
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0337916f8a
* Initial work on yara module * Adding in index basics * Updated the index stuff * Adding in proper tests * Fix editorconfig * Odd paths * that should do it * Fix tests * Fix tests * FFS * Once more * Mapping is not deterministic
32 lines
1.2 KiB
Text
32 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { YARA_INDEX } from '../../../../software/yara/index/main.nf' addParams( options: ['args': '-e 3'] )
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include { YARA_MAPPER } from '../../../../software/yara/mapper/main.nf' addParams( options: ['args': '-e 3'] )
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workflow test_yara_single_end {
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def fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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YARA_INDEX ( fasta )
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
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YARA_MAPPER ( input, YARA_INDEX.out.index )
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}
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workflow test_yara_paired_end {
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def fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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YARA_INDEX ( fasta )
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
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YARA_MAPPER ( input, YARA_INDEX.out.index )
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}
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