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5e18e36895
* Fixes for PR 371 * Fix tags * Add md5sum * Add md5sums for stringtie * Fix tests for modules where subtool = build * Fix pytest_software name conflicts * Change _ to / in test.yml tags * Nope...that didnt work * Fix sequenzautils/bam2seqz tests
29 lines
1.1 KiB
Text
29 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { STRINGTIE as STRINGTIE_FORWARD } from '../../../software/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
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include { STRINGTIE as STRINGTIE_REVERSE } from '../../../software/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
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/*
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* Test with forward strandedness
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*/
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workflow test_stringtie_forward {
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input = [ [ id:'test', strandedness:'forward' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ]
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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STRINGTIE_FORWARD ( input, 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 {
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input = [ [ id:'test', strandedness:'reverse' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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]
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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STRINGTIE_REVERSE ( input, gtf )
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}
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