fix: references correct

CCBR · Jun 12, 2024 · 79455d5 · 79455d5
1 parent e0317be
commit 79455d5
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Showing 4 changed files with 28 additions and 20 deletions.
diff --git a/modules/local/variant_calling.nf b/modules/local/variant_calling.nf
@@ -1,9 +1,9 @@
 GENOMEREF=file(params.genomes[params.genome].genome)
 GENOMEFAI=file(params.genomes[params.genome].genomefai)
 GENOMEDICT=file(params.genomes[params.genome].genomedict)
-KGPGERMLINE=params.genomes[params.genome].kgp
-DBSNP=file(params.genomes[params.genome].dbsnp)
+GERMLINE_RESOURCE=file(params.genomes[params.genome].germline_resource)
 GNOMADGERMLINE=params.genomes[params.genome].gnomad
+DBSNP=file(params.genomes[params.genome].dbsnp)
 PON=file(params.genomes[params.genome].pon)
 VEPCACHEDIR=file(params.genomes[params.genome].vepcache)
 VEPSPECIES=params.genomes[params.genome].vepspecies
@@ -75,7 +75,7 @@ process pileup_paired_t {
     """
     gatk --java-options -Xmx48g GetPileupSummaries \
         -I ${tumor} \
-        -V $KGPGERMLINE \
+        -V $GERMLINE_RESOURCE \
         -L ${bed} \
         -O ${tumorname}_${bed.simpleName}.tpileup.table
 
@@ -105,7 +105,7 @@ process pileup_paired_n {
     """
     gatk --java-options -Xmx48g GetPileupSummaries \
         -I ${normal} \
-        -V $KGPGERMLINE \
+        -V $GERMLINE_RESOURCE \
         -L ${bed} \
         -O ${normalname}_${bed.simpleName}.npileup.table
 

diff --git a/modules/local/variant_calling_tonly.nf b/modules/local/variant_calling_tonly.nf
@@ -1,9 +1,9 @@
 GENOMEREF=file(params.genomes[params.genome].genome)
 GENOMEFAI=file(params.genomes[params.genome].genomefai)
 GENOMEDICT=file(params.genomes[params.genome].genomedict)
-KGPGERMLINE=params.genomes[params.genome].kgp
-DBSNP=file(params.genomes[params.genome].dbsnp)
+GERMLINE_RESOURCE=file(params.genomes[params.genome].germline_resource)
 GNOMADGERMLINE=params.genomes[params.genome].gnomad
+DBSNP=file(params.genomes[params.genome].dbsnp)
 PON=file(params.genomes[params.genome].pon)
 VEPCACHEDIR=file(params.genomes[params.genome].vepcache)
 VEPSPECIES=params.genomes[params.genome].vepspecies
@@ -36,7 +36,7 @@ process pileup_paired_tonly {
     """
     gatk --java-options -Xmx48g GetPileupSummaries \
         -I ${tumor} \
-        -V $KGPGERMLINE \
+        -V $GERMLINE_RESOURCE \
         -L ${bed} \
         -O ${tumorname}_${bed.simpleName}.tpileup.table
 
@@ -207,8 +207,7 @@ process mutect2filter_tonly {
 
 
     """
-    gatk GatherVcfs -I ${mut2in} -O ${sample}.tonly.concat.vcf.gz
-    gatk IndexFeatureFile -I ${sample}.tonly.concat.vcf.gz
+    gatk SortVcf -I ${mut2in} -O ${sample}.tonly.concat.vcf.gz --CREATE_INDEX
     gatk FilterMutectCalls \
         -R $GENOMEREF \
         -V ${sample}.tonly.concat.vcf.gz \

diff --git a/subworkflows/local/workflows.nf b/subworkflows/local/workflows.nf
@@ -445,7 +445,9 @@ workflow VC {
         somaticcall_input=sage_in
     }else if("mutect2" in call_list){
         somaticcall_input=mutect2_in
-    }  
+    }else{
+        somaticcall_input=Channel.empty()
+    }
 
 
     //Implement PCGR Annotator/CivIC Next
@@ -460,24 +462,29 @@ workflow SV {
         bamwithsample
 
     main:
-        //Svaba
-        svaba_out=svaba_somatic(bamwithsample)
-        .map{ tumor,bps,contigs,discord,alignents,gindel,gsv,so_indel,so_sv,unfil_gindel,unfil_gsv,unfil_so_indel,unfil_sv,log ->
-            tuple(tumor,so_sv,"svaba")}
-        annotsv_svaba(svaba_out).ifEmpty("Empty SV input--No SV annotated")
+        svcall_list = params.svcallers.split(',') as List
 
+        if ("svaba" in svcall_list){
+        //Svaba
+            svaba_out=svaba_somatic(bamwithsample)
+            .map{ tumor,bps,contigs,discord,alignents,gindel,gsv,so_indel,so_sv,unfil_gindel,unfil_gsv,unfil_so_indel,unfil_sv,log ->
+                tuple(tumor,so_sv,"svaba")}
+            annotsv_svaba(svaba_out).ifEmpty("Empty SV input--No SV annotated")
+        }
+        if ("manta" in svcall_list){
         //Manta
         manta_out=manta_somatic(bamwithsample)
             .map{tumor,gsv,so_sv,unfil_sv,unfil_indel ->
             tuple(tumor,so_sv,"manta")}
         annotsv_manta(manta_out).ifEmpty("Empty SV input--No SV annotated")
-
+        }
         //Delly-WIP
 
-        //Survivor
-        gunzip(manta_out).concat(svaba_out).groupTuple()
-            | survivor_sv | annotsv_survivor_tn | ifEmpty("Empty SV input--No SV annotated")
-
+         if ("manta" in svcall_list & "svaba" in svcall_list){
+            //Survivor
+            gunzip(manta_out).concat(svaba_out).groupTuple()
+                | survivor_sv | annotsv_survivor_tn | ifEmpty("Empty SV input--No SV annotated")
+         }
 }
 
 workflow CNVmouse {

diff --git a/subworkflows/local/workflows_tonly.nf b/subworkflows/local/workflows_tonly.nf
@@ -245,6 +245,8 @@ workflow VC_TONLY {
         somaticcall_input=sage_in_tonly
     }else if("mutect2" in call_list){
         somaticcall_input=mutect2_in_tonly
+    }else{
+        somaticcall_input=Channel.empty()
     }
 
     emit: