Population_genomics_nextflow

/* WGS Analysis Pipeline
 *  Usage: Hackathon 2, BovReg- Nextflow workshop 17-20 Nov 2020
 *  Author: All hackathon participants
 *  
 */

// Setting some defaults here,
// can be overridden in config or via command line
params.reads="/home/ec2-user/environment/data/ggal/*_{1,2}.*fq"
params.ref="/home/ec2-user/environment/data/ggal/transcriptome.fa"
params.outdir="/home/ec2-user/environment/result_alignment"
params.out = "${params.outdir}/out"
//params.tmpdir = "${params.outdir}/gatk_temp"
//params.snpeff_data = "${params.outdir}/snpeff_data"

// Print some stuff here
println "reads: $params.reads"
println "ref: $params.ref"
println "output: $params.out"
//println "gatk temp dir: $params.tmpdir"
//println "snpeff db: $params.snpeff_db"
//println "snpeff data: $params.snpeff_data"

// Setup the reference file
ref = file(params.ref)

/* Prepare the fastq read pairs for input.
 * While doing this, count number of input samples
 */
num_samples = 0
Channel
    .fromFilePairs( params.reads )
    .ifEmpty { error "Cannot find any reads matching: ${params.reads}"  }
    .tap { read_pairs_ch }
    .subscribe({ num_samples += 1 })
    
    //read_pairs_ch.view()
    
process index {
    
    input:
    file transcriptome from ref
     
    output:
    //path 'index' into index_ch
    file("*") into index_ch

    script:       
    """
    bwa index ${transcriptome}
    """
}

//index_ch.view()


process align {
    cpus 1
  
    publishDir "${params.out}/aligned_reads", mode:'copy' // tells the output of the chanel it is created automatically by nextflow
	
    input:
    set pair_id, file(reads) from read_pairs_ch //the chanel creates the pair ids
    file(index) from index_ch
    
     
    output:
    set val(pair_id), file("${pair_id}_aligned_reads.sam") \
	into aligned_reads_ch
	
    script:
    """
    bwa mem ${ref} ${reads} > ${pair_id}_aligned_reads.sam
    """
    
}

aligned_reads_ch.view()