Merge pull request #115 from UMCUGenetics/release/v2.3.0

Release/v2.3.0

Author: rernst

CustomModules

@@ -93,7 +93,7 @@ process {
             path = "$params.outdir/QC/GenderCheck"
             mode = 'link'
         }
-    } 
+    }
 
     withLabel: CreateHSmetricsSummary {
         cpus = 2
@@ -112,8 +112,8 @@ process {
         time = { (1.ms * bam_file.size() / 1400) * task.attempt }
 
         publishDir = [
-            [path: "$params.outdir/exomedepth/UMCU", mode: 'link', pattern: 'UMCU*.vcf'],
-            [path: "$params.outdir/exomedepth/HC", mode: 'link', pattern: 'HC*.vcf'],
+            [path: "$params.outdir/exomedepth/UMCU", mode: 'link', pattern: '*_UMCU_*.vcf'],
+            [path: "$params.outdir/exomedepth/HC", mode: 'link', pattern: '*_HC_*.vcf'],
             [path: "$params.outdir/exomedepth/logs", mode: 'link', pattern: '*.log'],
             [path: "$params.outdir/exomedepth/igv_tracks", mode: 'link', pattern: '*.igv']
         ]
@@ -191,17 +191,24 @@ process {
         time = { 1.m * task.attempt }
     }
 
-    withLabel: GATK_3_8_1_0_gf15c1c3ef_CombineVariants {
+    withLabel: FranklinVCF {
         cpus = 2
         memory = { 5.GB * task.attempt }
-        time = { (1.ms * vcf_files.sum{it.size()} / 450) * task.attempt }
+        time = { 10.m * task.attempt }
 
         publishDir {
             path = "$params.outdir"
             mode = 'link'
+            saveAs = { filename -> filename.replace('.franklin.vcf', '.vcf')}
         }
     }
 
+    withLabel: GATK_3_8_1_0_gf15c1c3ef_CombineVariants {
+        cpus = 2
+        memory = { 5.GB * task.attempt }
+        time = { (1.ms * vcf_files.sum{it.size()} / 450) * task.attempt }
+    }
+
     withLabel: GATK_3_8_1_0_gf15c1c3ef_HaplotypeCaller {
         cpus = 2
         memory = { 10.GB * task.attempt }
@@ -228,6 +235,7 @@ process {
         publishDir {
             path = "$params.outdir/single_sample_vcf"
             mode = 'link'
+            saveAs = { filename -> filename.replace('.franklin.vcf', '.vcf')}
         }
     }
 
@@ -515,3 +523,9 @@ profiles {
         docker.runOptions = '-v /Users:/Users'
     }
 }
+
+nextflow {
+    enable {
+        moduleBinaries = true
+    }
+}

WES.config

@@ -106,6 +106,7 @@ include { SampleUDFDx as ClarityEpp_SampleGender } from './CustomModules/Clarity
     udf: 'Dx Geslacht', column_name: 'Gender', clarity_epp_path: params.clarity_epp_path
 )
 include { CompareGender } from './CustomModules/GenderCheck/CompareGender.nf'
+include { FranklinVCF } from './CustomModules/FranklinVCF/FranklinVCF.nf'
 
 
 def fastq_files = extractFastqPairFromDir(params.fastq_path)
@@ -146,8 +147,10 @@ workflow {
     )
     GATK_VariantFiltration(GATK_HaplotypeCaller.out)
     GATK_CombineVariants(GATK_VariantFiltration.out.groupTuple())
-    GATK_SingleSampleVCF(GATK_CombineVariants.out.combine(
-        Sambamba_Merge.out.map{sample_id, bam_file, bai_file -> [sample_id]})
+    FranklinVCF(GATK_CombineVariants.out)
+    GATK_SingleSampleVCF(
+        FranklinVCF.out.map{id, vcf_file -> [id, vcf_file, []]}
+        .combine(Sambamba_Merge.out.map{sample_id, bam_file, bai_file -> [sample_id]})
     )
 
     // GATK HaplotypeCaller (SNParray target)