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72e81d6e90
* Add spades module * Reorder gatk4 modules alphabetically * Update software/spades/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
52 lines
1.6 KiB
Text
52 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: [:] )
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workflow test_spades_single_end {
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def input = []
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def hmm = []
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def coronaspades = false
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ] ]
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SPADES ( input, hmm, coronaspades )
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}
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workflow test_spades_paired_end {
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def input = []
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def hmm = []
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def coronaspades = false
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] ]
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SPADES ( input, hmm, coronaspades )
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}
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workflow test_coronospades_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
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def hmm = []
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def coronaspades = true
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SPADES ( input, hmm, coronaspades )
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}
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workflow test_coronospades_paired_end {
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def input = []
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def hmm = []
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def coronaspades = true
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input = [ [ id:'test', single_end: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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SPADES ( input, hmm, coronaspades )
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}
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