mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
29 lines
1.5 KiB
Text
29 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { STAR_GENOMEGENERATE } from '../../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
|
|
include { STAR_ALIGN } from '../../../../software/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] )
|
|
|
|
workflow test_star_alignment_single_end {
|
|
|
|
def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
|
|
def gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
|
|
STAR_GENOMEGENERATE ( fasta, gtf )
|
|
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
|
|
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
|
|
}
|
|
|
|
workflow test_star_alignment_paired_end {
|
|
|
|
def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
|
|
def gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
|
|
STAR_GENOMEGENERATE ( fasta, gtf )
|
|
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
|
|
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
|
|
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
|
|
}
|