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Add split2 options

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This commit is contained in:
FriederikeHanssen 2021-02-22 22:43:32 +01:00
parent 5f9aa7264e
commit ec63f335d5
1 changed files with 39 additions and 5 deletions
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44
tests/software/seqkit/split2/main.nf
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@ -2,20 +2,54 @@
nextflow.enable.dsl = 2
include { SEQKIT_SPLIT2 } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: [:] )
include { SEQKIT_SPLIT2_LENGTH } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-length 2'] )
include { SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 2 ' ] )
include { SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 2 '] )
workflow test_seqkit_split2_single_end {
workflow test_seqkit_split2_length_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
SEQKIT_SPLIT2 ( input )
SEQKIT_SPLIT2_LENGTH ( input )
}
workflow test_seqkit_split2_paired_end {
workflow test_seqkit_split2_size_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
SEQKIT_SPLIT2_SIZE ( input )
}
workflow test_seqkit_split2_part_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
SEQKIT_SPLIT2_PART ( input )
}
workflow test_seqkit_split2_length_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
SEQKIT_SPLIT2 ( input )
SEQKIT_SPLIT2_LENGTH ( input )
}
workflow test_seqkit_split2_size_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
SEQKIT_SPLIT2_SIZE ( input )
}
workflow test_seqkit_split2_part_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
SEQKIT_SPLIT2_PART ( input )
}