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6d88f2da8c
* Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
46 lines
1.4 KiB
Text
46 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
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include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
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/*
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* Test with forward strandedness
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*/
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workflow test_stringtie_forward_merge {
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input = [
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[ id:'test', strandedness:'forward' ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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]
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annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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STRINGTIE_STRINGTIE ( input, annotation_gtf )
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STRINGTIE_STRINGTIE
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.out
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.transcript_gtf
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.map { it -> it[1] }
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.set { stringtie_gtf }
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STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
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}
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/*
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* Test with reverse strandedness
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*/
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workflow test_stringtie_reverse_merge {
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input = [
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[ id:'test', strandedness:'reverse' ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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]
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annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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STRINGTIE_STRINGTIE ( input, annotation_gtf )
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STRINGTIE_STRINGTIE
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.out
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.transcript_gtf
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.map { it -> it[1] }
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.set { stringtie_gtf }
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STRINGTIE_MERGE ( stringtie_gtf, annotation_gtf )
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}
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