Merge pull request #4 from ikmb/devel

Fixing various smaller issues

main.nf

@@ -54,7 +54,7 @@ if (params.pacbio) {
 
 	Channel.fromPath(params.samples)
 		.splitCsv(sep: ';', header: true)
-		.map{ row-> tuple( row.IndivID,row.SampleID,row.libraryID,row.rgID,row.platform_unit,row.platform,row.platform_model,row.center,row.run_date,file(row.R1),file(row.R1)  ) }
+		.map{ row-> tuple( row.IndivID,row.SampleID,row.libraryID,row.rgID,row.platform_unit,row.platform,row.platform_model,row.center,row.run_date,file(row.R1),file(row.R2)  ) }
 		.set { reads }
 }
 
@@ -102,10 +102,10 @@ workflow {
 		vcf = DEEPVARIANT_PACBIO.out.vcf
 		gvcf = DEEPVARIANT_PACBIO.out.gvcf
 	} else {
-		DEEPVARIANT_ILLUMINA(reads,bed,fastaGz,gzFai,gzi,fai)
-		bam = DEEPVARIANT_ILLUMINA.out.bam
-		vcf = DEEPVARIANT_ILLUMINA.out.vcf
-		gvcf = DEEPVARIANT_ILLUMINA.out.gvcf
+		DEEPVARIANT_SHORT_READS(reads,bed,fastaGz,gzFai,gzi,fai)
+		bam = DEEPVARIANT_SHORT_READS.out.bam
+		vcf = DEEPVARIANT_SHORT_READS.out.vcf
+		gvcf = DEEPVARIANT_SHORT_READS.out.gvcf
 	}
 
 	// effect prediction

modules/samtools/main.nf

@@ -6,8 +6,8 @@ process merge_and_dedup {
         tuple val(indivID), val(sampleID), path(aligned_bam_list)
 
         output:
-        tuple val(indivID),val(sampleID),path(merged_bam),path(merged_bam_index)
-        tuple path(merged_bam),path(merged_bam_index)
+        tuple val(indivID),val(sampleID),path(merged_bam),path(merged_bam_index), emit: bam
+        tuple path(merged_bam),path(merged_bam_index), emit: bam_simple
 
         script:
         merged_bam = indivID + "_" + sampleID + ".merged.md.cram"

nextflow.config

@@ -1,6 +1,7 @@
 params {
 
 	genome = "GRCh38"
+	pacbio = false 
 
 	run_name = false
 

workflows/deepvariant_illumina/main.nf

@@ -2,7 +2,7 @@ include { trim } from "./../../modules/fastp/main.nf" params(params)
 include { align } from "./../../modules/bwa/main.nf" params(params)
 include { merge_and_dedup } from "./../../modules/samtools/main.nf" params(params)
 include { deepvariant } from "./../../modules/deepvariant/main.nf" params(params)
-include { vcf_index ; vcf_pass } from "./../../modules/vcf/main.nf" params(params)
+include { vcf_add_dbsnp; vcf_index ; vcf_pass } from "./../../modules/vcf/main.nf" params(params)
 include { manta } from "./../../modules/sv/main.nf" params(params)
 include { bed_compress_and_index } from "./../../modules/htslib/main.nf" params(params)
 
@@ -29,6 +29,6 @@ workflow DEEPVARIANT_SHORT_READS {
 	emit:
 		gvcf = deepvariant.out[0]
 		vcf = vcf_add_dbsnp.out.mix(manta.out[0],manta.out[1],manta.out[2])
-		bam = merge_and_dedup.out
+		bam = merge_and_dedup.out.bam
 }