#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { STRINGTIE as STRINGTIE_F } from '../../../software/stringtie/main.nf'  addParams( options: [ publish_dir:'test_stringtie_forward' ] )
include { STRINGTIE as STRINGTIE_R } from '../../../software/stringtie/main.nf'  addParams( options: [ publish_dir:'test_stringtie_reverse' ] )

/*
 * Test with forward strandedness
 */
workflow test_stringtie_forward {

    def input = []
    input = [ [ id:'test', strandedness:'forward' ], // meta map
              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]

    STRINGTIE_F (
                    input,
                     file("${launchDir}/tests/data/gff/a.gtf", checkIfExists: true)
                     )
}

/*
 * Test with reverse strandedness
 */
workflow test_stringtie_reverse {

    def input = []
    input = [ [ id:'test', strandedness:'reverse' ], // meta map
              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]

    STRINGTIE_R (
                    input,
                     file("${launchDir}/tests/data/gff/a.gtf", checkIfExists: true)
                     )
}