nf-core_modules/tests/software/star/align/main.nf
Harshil Patel acb1a12a56
Re-organise all test data (#354)
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint
2021-03-24 09:53:41 +00:00

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 {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_single_end.fastq.gz", checkIfExists: true) ]
]
fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}
workflow test_star_alignment_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
]
fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}