rnaseq.nf

#!/usr/bin/env nextflow
VERSION="1.0"
nextflow.enable.dsl=2

// Include your modules and parameterize them
include { FASTQC }                from './modules/FASTQC' params(params)
include { TRIM_GALORE }           from './modules/TRIM_GALORE' params(params)
include { HISAT_INDEX }           from './modules/HISAT' params(params)
include { HISAT_MAPPING }         from './modules/HISAT' params(params)
include { FEATURE_COUNTS }        from './modules/QUANT' params(params)
include { FEATURE_COUNTS_MATRIX } from './modules/QUANT' params(params)
include { ESET }                  from './modules/QUANT' params(params)
include { MULTIQC }               from './modules/MULTIQC' params(params)

/*
// under construction (to replace load_reads)
def load_reads_from_csv(path, csv, paired) {
  if (paired) {
    Channel
      .fromPath(csv).splitCsv(header: true)
      .map {row -> [row.Sample_Name, [row.Read1, row.Read2]]}
      .ifEmpty {error "File ${csv} not parsed properly"}
      .into {reads;}
  } else {
    Channel
      .fromPath(params.reads).splitCsv(header: true)
      .map {row -> [row.Sample_Name, [row.Read1]]}
      .ifEmpty {error "File ${params.reads} not parsed properly"}
      .into {reads;}
  }
} 
*/
def load_reads(path, paired) {
  if (paired) {
    Channel
      .fromFilePairs( path )
      .set {reads}
  } else {
    Channel
      .fromPath( path )
      .map { [it.getName().split("\\_1|\\_2", 2)[0], [it]] }
      .set {reads}
  }
}
/**************************************************
* PAIRED-END RNA-SEQ
**************************************************/
workflow rnaseq_from_fastq_paired {
  load_reads("${params.wd}/raw_data/*_{R1,R2}*.fastq*.gz", params.paired)
  TRIM_GALORE( reads )
  HISAT_MAPPING( TRIM_GALORE.out[0] )
  FEATURE_COUNTS( HISAT_MAPPING.out[0], params.gtf)
  FEATURE_COUNTS_MATRIX( FEATURE_COUNTS.out[0].collect() )
  ESET( FEATURE_COUNTS_MATRIX.out[0] )
  MULTIQC( ESET.out[0] )
}

// create a hisat index
workflow hisat_index {
  HISAT_INDEX( params.fasta, params.gtf )
}

/**************************************************
* SINGLE-END RNA-SEQ
**************************************************/
workflow rnaseq_from_fastq_single {
  load_reads("${params.wd}/data/rnaseq/reads/*_1.fq.gz", params.paired)
  TRIM_GALORE( reads )
  HISAT_MAPPING( TRIM_GALORE.out[0] )
  FEATURE_COUNTS( HISAT_MAPPING.out[0], params.gtf)
  FEATURE_COUNTS_MATRIX( FEATURE_COUNTS.out[0].collect() )
  ESET( FEATURE_COUNTS_MATRIX.out[0] )
  MULTIQC( ESET.out[0] )
}

/**************************************************
* RNA-SEQ FROM BAM
**************************************************/
def load_bams(path) {
  Channel
      .fromPath( path )
      .map { [it.getName().split("\\.bam", 0)[0], [it]] }
      .set {bams}
}
workflow rnaseq_frombam {
  //load_bams("${params.outdir}/samples/ * /hisat/ *.bam")
  FEATURE_COUNTS( bams, params.gtf)
  FEATURE_COUNTS_MATRIX( FEATURE_COUNTS.out[0].collect() )
  ESET( FEATURE_COUNTS_MATRIX.out[0] )
  MULTIQC( ESET.out[0] )
}