Update haplochecker version in dockerfile and task to match (#5760)

* update haplochecker dockerfile and corresponding task, get rid of mitochondria dependencies zip, and update tests to match

scripts/m2_cromwell_tests/run_m2_wdl.sh

@@ -50,4 +50,7 @@ echo "Running M2 WDL through cromwell (Tumor-only)"
 sudo java -jar $CROMWELL_JAR run $WORKING_DIR/gatk/scripts/mutect2_wdl/mutect2_multi_sample.wdl -i $WORKING_DIR/test_m2_wdl_multi_mod_to.json -m $WORKING_DIR/test_m2_wdl_to.metadata
 
 echo "Running Mitochondria M2 WDL through cromwell"
-sudo java -jar $CROMWELL_JAR run $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl -i $WORKING_DIR/gatk/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json --imports $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/MitochondriaPipelineDependencies.zip -m $WORKING_DIR/test_mitochondria_m2_wdl.metadata
+ln -fs $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/AlignAndCall.wdl
+ln -fs $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
+ln -fs $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/MitochondriaCalling.wdl
+sudo java -jar $CROMWELL_JAR run $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl -i $WORKING_DIR/gatk/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json -m $WORKING_DIR/test_mitochondria_m2_wdl.metadata

scripts/mitochondria_m2_wdl/AlignAndCall.wdl

@@ -176,7 +176,7 @@ task GetContamination {
   Int map_qual = 30
   Float vaf = 0.01
 
-  String basename = basename(input_bam)
+  String basename = basename(input_bam, ".bam")
 
   # runtime
   Int? preemptible_tries
@@ -193,7 +193,7 @@ task GetContamination {
   command {
   set -e
 
-  java -jar /usr/mtdnaserver/mitolib-0.1.0.jar haplochecker \
+  java -jar /usr/mtdnaserver/mitolib.jar haplochecker \
     --in ${input_bam} \
     --ref ${ref_fasta} \
     --out haplochecker_out \
@@ -218,7 +218,7 @@ CODE
     preemptible: select_first([preemptible_tries, 5])
     memory: "3 GB"
     disks: "local-disk " + disk_size + " HDD"
-    docker: "gatkworkflows/mtdnaserver:1.0"
+    docker: "gatkworkflows/mtdnaserver:1.2"
   }
   output {
     File contamination_file = "haplochecker_out/${basename}.contamination.txt"

scripts/mitochondria_m2_wdl/Haplochecker/Dockerfile

@@ -9,4 +9,5 @@ RUN apt-get update && \
 WORKDIR /usr/mtdnaserver
 
 # Download mitolib jar
-RUN wget https://github.com/haansi/mitolib/releases/download/v0.1.0/mitolib-0.1.0.jar
+RUN wget https://github.com/haansi/mitolib/releases/download/0.1.2/mitolib-0.1.2.jar && \
+	mv mitolib-0.1.2.jar mitolib.jar