mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
33 lines
1.3 KiB
Text
33 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
|
|
include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_bowtie_index {
|
|
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
BOWTIE_INDEX ( fasta )
|
|
}
|
|
|
|
workflow test_bowtie_alignment_single_end {
|
|
|
|
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
BOWTIE_INDEX ( fasta )
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
|
|
BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
|
|
}
|
|
|
|
workflow test_bowtie_alignment_paired_end {
|
|
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
BOWTIE_INDEX ( fasta )
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
|
|
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
|
|
BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
|
|
}
|