Merge pull request #489 from nickhsmith/nf-core-dev

Nf core dev / variant calling bugs / ideas

bin/concatenateVCFs.sh

@@ -91,7 +91,7 @@ else
     bgzip -@${cpus} rawcalls.unsorted.vcf
 fi
 
-bcftools sort rawcalls.unsorted.vcf.gz | bgzip > rawcalls.vcf.gz
+bcftools sort -T . rawcalls.unsorted.vcf.gz | bgzip > rawcalls.vcf.gz
 tabix -p vcf rawcalls.vcf.gz
 
 set +u

conf/modules.config

@@ -471,6 +471,24 @@ process{
             path: { "${params.outdir}/variant_calling/${meta.sample}/haplotypecaller" }
         ]
     }
+    withName: 'HAPLOTYPECALLER' {
+        publishDir       = [
+            enabled: false,
+            mode: 'copy',
+            path: { "${params.outdir}/variant_calling/haplotypecaller"},
+            pattern: "*{vcf.gz,vcf.gz.tbi}"
+        ]
+        ext.args         = '-ERC GVCF'
+        ext.prefix        = {"${meta.id}.g"}
+    }
+    withName: 'GENOTYPEGVCFS' {
+        publishDir       = [
+            enabled: true,
+            mode: "${params.publish_dir_mode}",
+            path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller"},
+            pattern: "*{vcf.gz,vcf.gz.tbi}"
+        ]
+    }
     withName: 'CONCAT_VCF_MANTA_.*' {
         ext.args         = { params.no_intervals ?  "-n" : "" }
         ext.prefix       = {"${meta.sample}"}
@@ -540,9 +558,6 @@ process{
     //withName: 'GENOMICSDBIMPORT' {
     //
     //}
-    withName: 'HAPLOTYPECALLER' {
-        ext.args         = '-ERC GVCF'
-    }
     withName: 'MANTA_GERMLINE|MANTA_TUMORONLY|MANTA_SOMATIC' {
         ext.args         = { params.wes ? "--exome" : "" }
         publishDir       = [

modules.json

@@ -76,7 +76,7 @@
                 "git_sha": "967fb22dedc2c8855f00e64c3d7b5814c85242a6"
             },
             "gatk4/genotypegvcfs": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "871779213588426bf176d60d8307fe056143d5c0"
             },
             "gatk4/getpileupsummaries": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

nextflow_schema.json

@@ -768,4 +768,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}

subworkflows/local/germline_variant_calling.nf

@@ -24,6 +24,7 @@ include { DEEPVARIANT                                 } from '../../modules/nf-c
 include { FREEBAYES                                   } from '../../modules/nf-core/modules/freebayes/main'
 include { GATK_JOINT_GERMLINE_VARIANT_CALLING         } from '../../subworkflows/nf-core/joint_germline_variant_calling/main'
 include { GATK4_HAPLOTYPECALLER as HAPLOTYPECALLER    } from '../../modules/nf-core/modules/gatk4/haplotypecaller/main'
+include { GATK4_GENOTYPEGVCFS as GENOTYPEGVCFS        } from '../../modules/nf-core/modules/gatk4/genotypegvcfs/main'
 include { MANTA_GERMLINE                              } from '../../modules/nf-core/modules/manta/germline/main'
 include { STRELKA_GERMLINE                            } from '../../modules/nf-core/modules/strelka/germline/main'
 include { TIDDIT_SV                                   } from '../../modules/nf-core/modules/tiddit/sv/main'
@@ -62,6 +63,7 @@ workflow GERMLINE_VARIANT_CALLING {
     deepvariant_vcf       = Channel.empty()
     freebayes_vcf         = Channel.empty()
     haplotypecaller_gvcf  = Channel.empty()
+    genotypegvcfs_vcf     = Channel.empty()
     manta_vcf             = Channel.empty()
     strelka_vcf           = Channel.empty()
 
@@ -192,6 +194,7 @@ workflow GERMLINE_VARIANT_CALLING {
         if(no_intervals){
             TABIX_HAPLOTYPECALLER(HAPLOTYPECALLER.out.vcf)
             haplotypecaller_gvcf_gz = HAPLOTYPECALLER.out.vcf
+            haplotypecaller_gvcf_gz_tbi = HAPLOTYPECALLER.out.tbi
             ch_versions = ch_versions.mix(TABIX_HAPLOTYPECALLER.out.versions)
         }else{
             BGZIP_HAPLOTYPECALLER(HAPLOTYPECALLER.out.vcf)
@@ -205,11 +208,30 @@ workflow GERMLINE_VARIANT_CALLING {
 
             CONCAT_VCF_HAPLOTYPECALLER(haplotypecaller_gvcf_to_concat, fasta_fai, intervals_bed_combine_gz)
             haplotypecaller_gvcf_gz = CONCAT_VCF_HAPLOTYPECALLER.out.vcf
+            haplotypecaller_gvcf_gz_tbi = CONCAT_VCF_HAPLOTYPECALLER.out.tbi
 
             ch_versions = ch_versions.mix(BGZIP_HAPLOTYPECALLER.out.versions)
             ch_versions = ch_versions.mix(CONCAT_VCF_HAPLOTYPECALLER.out.versions)
         }
 
+        haplotypecaller_gvcf_gz.join(haplotypecaller_gvcf_gz_tbi)
+        .combine(intervals_bed_combine_gz_tbi)
+        .map{
+            meta, gvcf, gvf_tbi, intervals, intervals_tbi ->
+            new_intervals = intervals.simpleName != "no_intervals" ? intervals : []
+            new_intervals_tbi = intervals_tbi.simpleName != "no_intervals" ? intervals_tbi : []
+            [meta, gvcf, gvf_tbi, new_intervals, new_intervals_tbi]
+        }.set{haplotypecaller_gvcf_to_call}
+
+        genotypegvcfs_vcf_gz = GENOTYPEGVCFS(
+            haplotypecaller_gvcf_to_call,
+            fasta,
+            fasta_fai,
+            dict,
+            dbsnp,
+            dbsnp_tbi)
+
+        genotypegvcfs_vcf = genotypegvcfs_vcf.mix(genotypegvcfs_vcf_gz)
 
         if(joint_germline){
             run_haplotypecaller = false
@@ -236,7 +258,6 @@ workflow GERMLINE_VARIANT_CALLING {
         }
 
         haplotypecaller_gvcf = haplotypecaller_gvcf.mix(haplotypecaller_gvcf_gz)
-
     }
 
     if (tools.contains('manta')){
@@ -374,6 +395,7 @@ workflow GERMLINE_VARIANT_CALLING {
     deepvariant_vcf
     freebayes_vcf
     haplotypecaller_gvcf
+    genotypegvcfs_vcf
     manta_vcf
     strelka_vcf