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33 lines
1.6 KiB
Text
33 lines
1.6 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { HISAT2_EXTRACTSPLICESITES } from '../../../../software/hisat2/extractsplicesites/main.nf' addParams( options: [:] )
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include { HISAT2_BUILD } from '../../../../software/hisat2/build/main.nf' addParams( options: [:] )
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include { HISAT2_ALIGN } from '../../../../software/hisat2/align/main.nf' addParams( options: [:] )
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workflow test_hisat2_align_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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HISAT2_EXTRACTSPLICESITES ( gtf )
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HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
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HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
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}
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workflow test_hisat2_align_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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HISAT2_EXTRACTSPLICESITES ( gtf )
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HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
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HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
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}
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