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https://github.com/MillironX/nf-core_modules.git
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6ad50f8ec4
* add stringtie merge module * add md5sum and path for stringtie.merged.gtf * fix errors * try fixing stringtie check error * add tag * remove unreproducible md5sum * address PR suggestions * hopefully fix linting error
38 lines
1.9 KiB
Text
38 lines
1.9 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/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
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include { STRINGTIE as STRINGTIE_REVERSE } from '../../../../software/stringtie/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
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include { STRINGTIE_MERGE as STRINGTIE_FORWARD_MERGE} from '../../../../software/stringtie/merge/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward_merge'] )
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include { STRINGTIE_MERGE as STRINGTIE_REVERSE_MERGE} from '../../../../software/stringtie/merge/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse_merge'] )
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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 = [ [ 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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annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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STRINGTIE_FORWARD ( input, annotation_gtf )
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STRINGTIE_FORWARD.out.transcript_gtf
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.map { it -> it[1] }
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.set { stringtie_gtf }
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STRINGTIE_FORWARD_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 = [ [ 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_REVERSE ( input, annotation_gtf )
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STRINGTIE_REVERSE.out.transcript_gtf
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.map { it -> it[1] }
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.set { stringtie_gtf }
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STRINGTIE_REVERSE_MERGE ( stringtie_gtf, annotation_gtf )
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}
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