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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
ramdaq
========================================================================================
Github : https://github.com/rikenbit/ramdaq
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
========================================================================================
GENOME PARAMETER VALUES
========================================================================================
*/
/*
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
params.gff = WorkflowMain.getGenomeAttribute(params, 'gff')
params.gene_bed = WorkflowMain.getGenomeAttribute(params, 'bed12')
params.bbsplit_index = WorkflowMain.getGenomeAttribute(params, 'bbsplit')
params.star_index = WorkflowMain.getGenomeAttribute(params, 'star')
params.hisat2_index = WorkflowMain.getGenomeAttribute(params, 'hisat2')
params.rsem_index = WorkflowMain.getGenomeAttribute(params, 'rsem')
params.salmon_index = WorkflowMain.getGenomeAttribute(params, 'salmon')
*/
/*
adapter = "${params.local_annot_dir}/all_sequencing_WTA_adopters.fa"
hisat2_idx = "${params.local_annot_dir}/hisat2_v220_index_GRCm39_primary_ERCC/*.ht2"
hisat2_rrna_idx = "${params.local_annot_dir}/hisat2_index_Mouse_rRNA_12_mito_5_45.tar.gz"
chrsize = "${params.local_annot_dir}/GRCm39.primary_assembly.genome.fa.fai"
bed = "${params.local_annot_dir}/gencode.vM26.primary_assembly.annotation.bed"
gtf = "${params.local_annot_dir}/gencode.vM26.primary_assembly.annotation.ERCC.gtf"
mt_gtf = "${params.local_annot_dir}/gencode.vM26.primary_assembly.annotation.mt.gtf"
rrna_gtf = "${params.local_annot_dir}/Mouse_GRCm39_rmsk_rRNA_Refseq_45S_merge.gtf"
histone_gtf = "${params.local_annot_dir}/gencode.vM26.primary_assembly.annotation.histone.gtf"
hisat2_sirv_idx = "${params.local_annot_dir}/hisat2_v220_index_SIRVome/*.ht2"
rsem_sirv_idx = "${params.local_annot_dir}/RSEM_bowtie2_index_SIRVome/*"
rsem_allgene_idx = "${params.local_annot_dir}/RSEM_bowtie2_index_gencode_vM26/*"
*/
/*
========================================================================================
VALIDATE & PRINT PARAMETER SUMMARY
========================================================================================
*/
//WorkflowMain.initialise(workflow, params, log)
/*
========================================================================================
RUN WORKFLOWS
========================================================================================
*/
include { RAMDAQ } from './workflows/ramdaq'
//
// WORKFLOW: Run main ramdaq analysis pipeline
//
workflow {
RAMDAQ ()
}
/*
========================================================================================
THE END
========================================================================================
*/