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

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2021-01-22 13:01:59 +00:00
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: [:] )
include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [:] )
workflow test_star_genomegenerate {
fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
}
// workflow test_star_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_star_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 )
// }