nf-core_modules/tests/software/stringtie/merge/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STRINGTIE as STRINGTIE_FORWARD } from '../../../../software/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
include { STRINGTIE as STRINGTIE_REVERSE } from '../../../../software/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
include { STRINGTIE_MERGE as STRINGTIE_FORWARD_MERGE} from '../../../../software/stringtie/merge/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward_merge'] )
include { STRINGTIE_MERGE as STRINGTIE_REVERSE_MERGE} from '../../../../software/stringtie/merge/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse_merge'] )
/*
* Test with forward strandedness
*/
workflow test_stringtie_forward_merge {
input = [ [ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE_FORWARD ( input, annotation_gtf )
STRINGTIE_FORWARD.out.transcript_gtf
.map { it -> it[1] }
.set { stringtie_gtf }
STRINGTIE_FORWARD_MERGE ( stringtie_gtf, annotation_gtf )
}
/*
* Test with reverse strandedness
*/
workflow test_stringtie_reverse_merge {
input = [ [ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE_REVERSE ( input, annotation_gtf )
STRINGTIE_REVERSE.out.transcript_gtf
.map { it -> it[1] }
.set { stringtie_gtf }
STRINGTIE_REVERSE_MERGE ( stringtie_gtf, annotation_gtf )
}