vcf_in_bgen_merge.nf

/*
 * Authors       :
 *
 *
 *      Scott Hazelhurst
 *      jean-tristan Brandenburg
 *
 *  On behalf of the H3ABionet Consortium
 *  2015-2019
 *
 *
 * Description  : Nextflow pipeline to transform vcf file in plink and other format
 *
 *(C) University of the Witwatersrand, Johannesburg, 2016-2019 on behalf of the H3ABioNet Consortium
 *This is licensed under the MIT Licence. See the "LICENSE" file for details
 */

//---- General definitions --------------------------------------------------//


import java.nio.file.Paths;
import sun.nio.fs.UnixPath;
import java.security.MessageDigest;


def helps = [ 'help' : 'help' ]
allowed_params = ['file_listvcf', 'min_scoreinfo', "output_dir", "max_cores"]

params.mem_req = '10GB' // how much plink needs for this
params.output_dir="bgen/"
params.output="bgen"
params.file_listvcf=""
params.min_scoreinfo=0.6
params.max_cores = 8
params.genotype_field="GP"
params.qctoolsv2_bin="qctool_v2"
params.bcftools_bin="bcftools"
params.score_imp="INFO"


if(params.file_listvcf==""){
error('params.file_listvcf : file contains list vcf not found')
}
list_vcf=Channel.fromPath(file(params.file_listvcf).readLines())

process filter_vcf{
  cpus params.max_cores
  memory params.mem_req
  time   params.big_time
  input :
     file(vcf) from list_vcf
  output :
     set file("${Ent}"), file("${Ent}.csi") into list_vcf_filt
  script :
    Ent=vcf.baseName+"_filter.vcf.gz"
    """
    ${params.bcftools_bin} view -i '${params.score_imp}>${params.min_scoreinfo}' $vcf -Oz > $Ent
    ${params.bcftools_bin} index $Ent
    """
}
lcf=list_vcf_filt.collect()

process mergeall{
  time   params.big_time
  memory params.mem_req
  input :
     file(allfile) from lcf
  output :
     file("$out") into merge_vcf
   script :
    out="all.vcf.gz"
    """
    ${params.bcftools_bin} concat *vcf.gz -Oz -o $out
    """
    
}
process formatvcfinbgen{
  cpus params.max_cores
  memory params.mem_req
  time   params.big_time
  input :
     file(vcf) from merge_vcf
  publishDir "${params.output_dir}/", overwrite:true, mode:'copy'
  output :
     file("${Ent}.bgen")
  script :
    Ent="${params.output}"
    """
    ${params.qctoolsv2_bin} -g $vcf -vcf-genotype-field ${params.genotype_field} -ofiletype bgen -og ${Ent}.bgen -filetype vcf 
    """
}