mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
33 lines
1.3 KiB
Text
33 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] )
|
|
include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_bowtie2_build {
|
|
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
BOWTIE2_BUILD ( fasta )
|
|
}
|
|
|
|
workflow test_bowtie2_alignment_single_end {
|
|
|
|
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
BOWTIE2_BUILD ( fasta )
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
|
|
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
|
|
}
|
|
|
|
workflow test_bowtie2_alignment_paired_end {
|
|
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
BOWTIE2_BUILD ( 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) ] ]
|
|
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
|
|
}
|