mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
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
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { STAR_GENOMEGENERATE } from '../../../modules/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 11'] )
|
|
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'] )
|
|
include { ARRIBA } from '../../../modules/arriba/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_arriba_single_end {
|
|
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
|
|
|
STAR_GENOMEGENERATE ( fasta, gtf )
|
|
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
|
|
ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
|
|
}
|
|
|
|
workflow test_arriba_paired_end {
|
|
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
|
|
|
STAR_GENOMEGENERATE ( fasta, gtf )
|
|
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
|
|
ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
|
|
}
|