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aa76c6d870
* add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
35 lines
1.2 KiB
Text
35 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ADAPTERREMOVAL } from '../../../software/adapterremoval/main.nf' addParams( options: [:] )
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workflow test_adapterremoval_single_end {
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def input = []
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input = [ [ id:'test', single_end:true, collapse:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
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ADAPTERREMOVAL ( input )
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}
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workflow test_adapterremoval_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false, collapse:false ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ]]
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ADAPTERREMOVAL ( input )
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}
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workflow test_adapterremoval_paired_end_collapse {
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def input = []
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input = [ [ id:'test', single_end:false, collapse:true ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ]]
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ADAPTERREMOVAL ( input )
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}
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