From 0ef17df25b27183ee5b5ada81df11053f3e7fd40 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Wed, 29 Nov 2023 11:19:08 -0500 Subject: [PATCH] fix: revert back to DISCVR --- docker/logan_base/Dockerfile | 23 +++++------------------ workflow/modules/variant_calling.nf | 14 +++++++------- workflow/modules/variant_calling_tonly.nf | 4 ++-- 3 files changed, 14 insertions(+), 27 deletions(-) diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index 5182c64..f0b2eca 100644 --- 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 index 1e6bb0a..d7b3bf9 100644 --- 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 index 81a35c7..3d67e26 100644 --- 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 \