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22 lines
1 KiB
Text
22 lines
1 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { RSEM_PREPAREREFERENCE } from '../../../../software/rsem/preparereference/main.nf' addParams(options: [args: "--star"])
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include { RSEM_CALCULATEEXPRESSION } from '../../../../software/rsem/calculateexpression/main.nf' addParams(options: [args: "--star --star-gzipped-read-file"])
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workflow test_rsem_calculateexpression {
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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input = [ [ id:'test', single_end:false, strandedness: 'forward' ], // 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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RSEM_PREPAREREFERENCE ( fasta, gtf )
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RSEM_CALCULATEEXPRESSION( input, RSEM_PREPAREREFERENCE.out.index )
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}
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