fix: revert back to DISCVR

CCBR · Nov 29, 2023 · 0ef17df · 0ef17df
1 parent 971f08a
commit 0ef17df
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Showing 3 changed files with 14 additions and 27 deletions.
diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile
@@ -20,7 +20,8 @@ WORKDIR /opt2
 RUN apt-get update \
  && apt-get -y upgrade \
  && DEBIAN_FRONTEND=noninteractive apt-get install -y \
-      bc
+      bc \
+      openjdk-17-jdk   
 
 # Common bioinformatics tools 
 # bwa/0.7.17-4  bowtie/1.2.3  bowtie2/2.3.5.1 
@@ -44,23 +45,9 @@ RUN wget https://github.com/biod/sambamba/releases/download/v0.8.1/sambamba-0.8.
     && mv /opt2/sambamba-0.8.1-linux-amd64-static /opt2/sambamba \
     && chmod a+rx /opt2/sambamba
 
-# Install GATK4 (GATK/4.3.0.0)
-# Requires Java8 or 1.8
-RUN wget https://github.com/broadinstitute/gatk/releases/download/4.3.0.0/gatk-4.3.0.0.zip \
-    && unzip /opt2/gatk-4.3.0.0.zip \
-    && rm /opt2/gatk-4.3.0.0.zip \
-    && /opt2/gatk-4.3.0.0/gatk --list
-ENV PATH="/opt2/gatk-4.3.0.0:$PATH"
-
-# Install last release of GATK3 (GATK/3.8-1)
-# Only being used for the CombineVariants
-# command that is not available in GATK4
-# Available via env variable: $GATK_JAR
-# Requires Java8 or 1.8
-RUN wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2 \
-    && tar -xvjf /opt2/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2 \
-    && rm /opt2/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2
-ENV GATK_JAR="/opt2/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar"
+# Use DISCVRSeq For CombineVariants Replacement
+RUN wget https://github.com/BimberLab/DISCVRSeq/releases/download/1.3.61/DISCVRSeq-1.3.62.jar 
+ENV DISCVRSeq_JAR="/opt2/DISCVRSeq-1.3.62.jar"
 
 # Install dependencies needed to add a new repository over HTTPS
 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y \

diff --git a/workflow/modules/variant_calling.nf b/workflow/modules/variant_calling.nf
@@ -744,13 +744,13 @@ process somaticcombine {
     script:
         vcfin1=[callers, vcfs].transpose().collect { a, b -> a + " " + b }
         vcfin2="-V:" + vcfin1.join(" -V:")
-
-    """    
-    java  -jar \$GATK_JAR -T CombineVariants \
-        -nt $task.cpus \
-        --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED \
-        --genotypemergeoption PRIORITIZE \
-        --rod_priority_list mutect2,strelka,muse,lofreq,vardict,varscan \
+    
+    """
+    java -jar \$DISCVRSeq_JAR MergeVcfsAndGenotypes \
+        -R $GENOMEREF \
+        --genotypeMergeOption PRIORITIZE \
+        --priority_list mutect2,strelka,octopus,muse,lofreq,vardict,varscan \
+        --filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED \
         -O ${tumorsample}_vs_${normal}_combined.vcf.gz \
         $vcfin2
     """

diff --git a/workflow/modules/variant_calling_tonly.nf b/workflow/modules/variant_calling_tonly.nf
@@ -364,8 +364,8 @@ process somaticcombine_tonly {
         vcfin2="-V:" + vcfin1.join(" -V:")
 
     """
-    java -jar \$GATK_JAR -T CombineVariants \
-        -nt $task.cpus \
+    java -jar \$DISCVRSeq_JAR MergeVcfsAndGenotypes \
+        -R $GENOMEREF \
         --genotypeMergeOption PRIORITIZE \
         --priority_list mutect2_tonly,octopus_tonly,vardict_tonly,varscan_tonly \
         --filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED \