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3cabc95d0e
* Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
36 lines
2.3 KiB
Text
36 lines
2.3 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' addParams( options: [args: '--genomeSAindexNbases 11'] )
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include { STAR_ALIGN } from '../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'] )
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include { ARRIBA } from '../../../modules/arriba/main.nf' addParams( options: [:] )
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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_GENOMEGENERATE ( fasta, gtf )
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
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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_GENOMEGENERATE ( fasta, gtf )
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
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ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
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}
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