nf-core_modules/tests/software/samtools/main.nf

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