Merge pull request #132 from hartwigmedical/DEV-1154

DEV-1154: Bump AMBER to 3.2
hartwigmedical · Feb 24, 2020 · 9134af5 · 9134af5
2 parents 60828d6 + 5df8927
commit 9134af5
Show file tree

Hide file tree

Showing 4 changed files with 12 additions and 15 deletions.
diff --git a/cluster/src/main/java/com/hartwig/pipeline/tertiary/amber/Amber.java b/cluster/src/main/java/com/hartwig/pipeline/tertiary/amber/Amber.java
@@ -39,8 +39,7 @@ public List<BashCommand> commands(final SomaticRunMetadata metadata) {
                 metadata.tumor().sampleName(),
                 getTumorBamDownload().getLocalTargetPath(),
                 Resource.REFERENCE_GENOME_FASTA,
-                Resource.of(ResourceNames.AMBER_PON, "GermlineHetPon.hg19.bed"),
-                Resource.of(ResourceNames.AMBER_PON, "GermlineSnp.hg19.bed")));
+                Resource.of(ResourceNames.AMBER_PON, "GermlineHetPon.hg19.vcf.gz")));
     }
 
     @Override

diff --git a/cluster/src/main/java/com/hartwig/pipeline/tertiary/amber/AmberApplicationCommand.java b/cluster/src/main/java/com/hartwig/pipeline/tertiary/amber/AmberApplicationCommand.java
@@ -5,7 +5,7 @@
 
 class AmberApplicationCommand extends HmfToolCommand {
     AmberApplicationCommand(String referenceSampleName, String referenceBamPath, String tumorSampleName, String tumorBamPath,
-            String referenceGenomePath, String bedPath, String snpBedPath) {
+            String referenceGenomePath, String lociPath) {
         super("amber",
                 Versions.AMBER,
                 "amber.jar",
@@ -17,9 +17,7 @@ class AmberApplicationCommand extends HmfToolCommand {
                 tumorBamPath,
                 "-ref_genome",
                 referenceGenomePath,
-                "-bed",
-                bedPath,
-                "-snp_bed",
-                snpBedPath);
+                "-loci",
+                lociPath);
     }
 }
diff --git a/cluster/src/main/java/com/hartwig/pipeline/tools/Versions.java b/cluster/src/main/java/com/hartwig/pipeline/tools/Versions.java
@@ -1,13 +1,13 @@
 package com.hartwig.pipeline.tools;
 
-import org.jetbrains.annotations.NotNull;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
 import java.util.stream.Stream;
 
+import org.jetbrains.annotations.NotNull;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 public interface Versions {
 
     String BWA = "0.7.17";
@@ -19,7 +19,7 @@ public interface Versions {
     String SNPEFF = "4.3s";
     String STRELKA_POST_PROCESS = "1.6";
     String TABIX = "0.2.6";
-    String AMBER = "2.5";
+    String AMBER = "3.2";
     String COBALT = "1.7";
     String HEALTH_CHECKER = "3.1";
     String PURPLE = "2.39";

diff --git a/cluster/src/test/java/com/hartwig/pipeline/tertiary/amber/AmberTest.java b/cluster/src/test/java/com/hartwig/pipeline/tertiary/amber/AmberTest.java
@@ -26,11 +26,11 @@ protected Stage<AmberOutput, SomaticRunMetadata> createVictim() {
 
     @Override
     protected List<String> expectedCommands() {
-        return Collections.singletonList("java -Xmx32G -cp /opt/tools/amber/2.5/amber.jar com.hartwig.hmftools.amber.AmberApplication "
+        return Collections.singletonList("java -Xmx32G -cp /opt/tools/amber/3.2/amber.jar com.hartwig.hmftools.amber.AmberApplication "
                 + "-reference reference -reference_bam /data/input/reference.bam -tumor tumor -tumor_bam /data/input/tumor.bam -output_dir "
                 + "/data/output -threads $(grep -c '^processor' /proc/cpuinfo) -ref_genome "
-                + "/opt/resources/reference_genome/Homo_sapiens.GRCh37.GATK.illumina.fasta -bed "
-                + "/opt/resources/amber_pon/GermlineHetPon.hg19.bed -snp_bed /opt/resources/amber_pon/GermlineSnp.hg19.bed");
+                + "/opt/resources/reference_genome/Homo_sapiens.GRCh37.GATK.illumina.fasta "
+                + "-loci /opt/resources/amber_pon/GermlineHetPon.hg19.vcf.gz");
     }
 
     @Override