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42 lines
2 KiB
Text
42 lines
2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { STAR_GENOMEGENERATE } from '../../../modules/star/genomegenerate/main.nf'
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include { STAR_ALIGN } from '../../../modules/star/align/main.nf'
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include { ARRIBA } from '../../../modules/arriba/main.nf'
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workflow test_arriba_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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star_ignore_sjdbgtf = false
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seq_platform = 'illumina'
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seq_center = false
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STAR_GENOMEGENERATE ( fasta, gtf )
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
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ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf , [], [], [], [], [])
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}
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workflow test_arriba_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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star_ignore_sjdbgtf = false
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seq_platform = 'illumina'
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seq_center = false
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STAR_GENOMEGENERATE ( fasta, gtf )
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
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ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf, [], [], [], [], [])
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}
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