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3d720a24fd
* Add allelecount module * Add bed file input * Added bai file * Changed conda version * Update main.nf * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Add allelecount module * Add bed file input * Added bai file * Changed conda version * Update main.nf * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Remove newline * Fix pytest_software.yml * Update pytest_software.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
14 lines
641 B
Text
14 lines
641 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ALLELECOUNTER } from '../../../software/allelecounter/main.nf' addParams( options: [:] )
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workflow test_allelecounter {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)]
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positions = [ file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
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ALLELECOUNTER ( input, positions )
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}
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