nextflow.enable.dsl = 2

include {FASTQC} from './modules/fastqc'

include {BWAMEM} from './modules/bwamem'

include {MERGEB} from './modules/mergeb'

include {ELPREP} from './modules/elprep'

include {SAMTOOLS} from './modules/samtools'

include {QUALIMAP} from './modules/qualimap'

include {B2C} from './modules/b2c'

include {STRELKA_ONESAMPLE} from './modules/strelka'

include {STRELKA_POOL} from './modules/strelka'

include {BCFTOOLS_FILTER; BCFTOOLS_FILTER as BF} from './modules/bcftools'

include {ANNOVAR as ANNOVAR_DS} from './modules/annovar'

include {ANNOVAR as ANNOVAR_DP} from './modules/annovar'

include {ANNOVAR as ANNOVAR_SS} from './modules/annovar'

include {ANNOVAR as ANNOVAR_SP} from './modules/annovar'

include {MULTIQC} from './modules/multiqc'

include {DEEPVARIANT_ONESAMPLE} from './modules/deepvariant'

include {GLNEXUS_DEEPVARIANT} from './modules/glnexus'

include {B2V} from './modules/b2v'

process PRINT_VERSIONS {

publishDir "$params.outdir/software", mode: "copy"

output:

path("versions.txt")

"""

}

workflow {

// TODO do a parameter check

PRINT_VERSIONS()

//we read pairs from regex

if(params.csv != null){

//we reads pairs from csv

read_pairs_ch=Channel.fromPath(params.csv) \

| splitCsv(header:true) \

| map { row-> tuple(row.sampleId, row.part, file(row.read1), file(row.read2))}\

}else{

println "Error: reads regex or path"

}

read_pairs_ch.view()

//fastqc read quality

FASTQC(read_pairs_ch)

//read aligment alt/hla

BWAMEM(read_pairs_ch)

//we do merge the bams by sample ID

groups=BWAMEM.out.bams.groupTuple(by: 0)

MERGEB(groups)

MERGEB.out.mbams.view()

//bam procesisng sort/duplciates/bqrs

SAMTOOLS(MERGEB.out.mbams)

//Quality of alignments

SAMTOOLS.out.bams.view()

QUALIMAP(SAMTOOLS.out.bams)

//BAM->CRAM conversion

B2C(SAMTOOLS.out.bams)

//Strelka to call variants

STRELKA_ONESAMPLE(SAMTOOLS.out.bams)

//we prepare samples for running strelka pool

bams = SAMTOOLS.out.bams.map {it -> it[1]}.collect()

bais = SAMTOOLS.out.bams.map {it -> it[2]}.collect()

STRELKA_POOL("Strelka",bams,bais)

BCFTOOLS_FILTER(STRELKA_ONESAMPLE.out.vcf)

//we filter pool variants

BF(STRELKA_POOL.out.vcf)

//DeepVariant to call variants - single sample

DEEPVARIANT_ONESAMPLE(SAMTOOLS.out.bams)

DEEPVARIANT_ONESAMPLE.out.gvcf.view()

gvcfs = DEEPVARIANT_ONESAMPLE.out.gvcf.map {it -> it[1]}.collect()

// glnexus to merge variants - pool DeepVariants

GLNEXUS_DEEPVARIANT("DeepVariant",gvcfs)

GLNEXUS_DEEPVARIANT.out.bcf.view()

//bcf to vcf

B2V(GLNEXUS_DEEPVARIANT.out.bcf)

//Annotation with ANNOVAR

ANNOVAR_DP(B2V.out.vcf,"DP")

ANNOVAR_DS(DEEPVARIANT_ONESAMPLE.out.vcf,"DS")

ANNOVAR_SP(BF.out.vcf,"SP")

ANNOVAR_SS(BCFTOOLS_FILTER.out.vcf,"SS")

//MiltiQC for metrics

MULTIQC(baseDir)

}