2021-02-03 16:02:58 +00:00
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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2021-11-26 07:58:40 +00:00
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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 { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../modules/star/align/main.nf'
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include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../modules/star/align/main.nf'
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2021-02-03 16:02:58 +00:00
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workflow test_star_alignment_single_end {
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2021-11-26 07:58:40 +00:00
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input = [
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[ 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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2021-07-21 12:30:52 +00:00
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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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2021-11-26 07:58:40 +00:00
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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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2021-03-24 09:53:41 +00:00
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STAR_GENOMEGENERATE ( fasta, gtf )
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2021-11-26 07:58:40 +00:00
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
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2021-02-03 16:02:58 +00:00
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}
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workflow test_star_alignment_paired_end {
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2021-11-26 07:58:40 +00:00
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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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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]
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2021-07-21 12:30:52 +00:00
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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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2021-11-26 07:58:40 +00:00
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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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2021-02-03 16:02:58 +00:00
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STAR_GENOMEGENERATE ( fasta, gtf )
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2021-11-26 07:58:40 +00:00
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
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2021-02-03 16:02:58 +00:00
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}
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2021-07-21 12:30:52 +00:00
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workflow test_star_alignment_paired_end_for_fusion {
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2021-11-26 07:58:40 +00:00
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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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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]
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2021-07-21 12:30:52 +00:00
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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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2021-11-26 07:58:40 +00:00
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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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2021-07-21 12:30:52 +00:00
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STAR_GENOMEGENERATE ( fasta, gtf )
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2021-11-26 07:58:40 +00:00
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STAR_FOR_ARRIBA ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
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2021-07-21 12:30:52 +00:00
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}
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2021-07-26 17:03:30 +00:00
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workflow test_star_alignment_paired_end_for_starfusion {
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2021-11-26 07:58:40 +00:00
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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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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]
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2021-07-26 17:03:30 +00:00
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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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2021-11-26 07:58:40 +00:00
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star_ignore_sjdbgtf = false
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seq_platform = false
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seq_center = false
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2021-07-26 17:03:30 +00:00
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STAR_GENOMEGENERATE ( fasta, gtf )
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2021-11-26 07:58:40 +00:00
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STAR_FOR_STARFUSION ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
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2021-07-26 17:03:30 +00:00
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}
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