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80 lines
2.9 KiB
Text
80 lines
2.9 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
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include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
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include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
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include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
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include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
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include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] )
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include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] )
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workflow test_samtools_flagstat {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
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SAMTOOLS_FLAGSTAT ( input )
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}
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workflow test_samtools_idxstats {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
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SAMTOOLS_IDXSTATS ( input )
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}
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workflow test_samtools_index {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
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SAMTOOLS_INDEX ( input )
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}
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// FIXME Why is this passing it an already sorted bam?
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workflow test_samtools_sort {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
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SAMTOOLS_SORT ( input )
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}
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workflow test_samtools_stats {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
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SAMTOOLS_STATS ( input )
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}
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workflow test_samtools_view {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
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SAMTOOLS_VIEW ( input )
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}
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workflow test_samtools_mpileup {
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def input = []
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def fasta = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
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fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
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SAMTOOLS_MPILEUP ( input, fasta )
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}
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