Make MELT scripts independent of the execution path.

dockerfiles/melt/run_MELT_2.0.5.sh

@@ -19,7 +19,7 @@ set -euo pipefail
 ##### Usage statement
 usage(){
 cat <<EOF
-  usage: runMELT.sh bam ref cov read_len mean_is MELT_DIR RUN_DIR REF_VER
+  usage: runMELT.sh bam ref cov read_len mean_is MELT_DIR REF_VER
   Runs MELT for mobile element detection. Requires paired-end deep (>10X) WGS data mapped with BWA.
   Positional arguments (all required):
     bam        Full path to mapped bam file (bam.bai assumed accompanying the BAM)
@@ -28,15 +28,14 @@ cat <<EOF
     read_len   Mean read length of library
     mean_is    Mean insert size of library
     MELT_DIR   Full path to MELT install directory
-    RUN_DIR    Full path to directory for MELT output
     REF_VER    Reference version (19|38)
 EOF
 }
 
 ##### Args parsing and validation
 if [[ "$#" -eq 0 ]]; then
   usage && exit 0;
-elif [[ "$#" -lt 8 ]]; then
+elif [[ "$#" -lt 7 ]]; then
   echo "At least one of the required parameters is not properly set by the given command:"
   temp_args="$@" && echo "$0 ${temp_args}" && exit 1;
 fi
@@ -51,11 +50,10 @@ cov=$3
 read_len=$4
 mean_is=$5
 MELT_DIR=$6
-RUN_DIR=$7
-REF_VER=$8
+REF_VER=$7
 
 ##### Check for required input (unset or empty)
-if [ -z "${bam}" ] || [ -z "${ref}" ] || [ -z "${cov}" ] || [ -z "${read_len}" ] || [ -z "${mean_is}" ] || [ -z "${MELT_DIR}" ] || [ -z "${RUN_DIR}" ] || [ -z "${REF_VER}" ]; then
+if [ -z "${bam}" ] || [ -z "${ref}" ] || [ -z "${cov}" ] || [ -z "${read_len}" ] || [ -z "${mean_is}" ] || [ -z "${MELT_DIR}" ] || [ -z "${REF_VER}" ]; then
   echo "At least one of the required parameters is not properly set by the given command:"
   temp_args="$@" && echo "$0 ${temp_args}" && exit 1; # non-zero exit because it indicates user errror
 fi
@@ -76,20 +74,18 @@ read_len=$( echo "${read_len}" | cut -f1 -d\. )
 mean_is=$( echo "${mean_is}" | cut -f1 -d\. )
 
 ##### remove trailing slash just to make sure
-RUN_DIR="${RUN_DIR%/}"
 MELT_DIR="${MELT_DIR%/}"
 
 ##### Create transposons reference list
 if [[ "$REF_VER" == "38" ]]; then
-  ls "${MELT_DIR}"/me_refs/Hg38/*zip | sed 's/\*//g' > "${RUN_DIR}/transposon_reference.list"
+  ls "${MELT_DIR}"/me_refs/Hg38/*zip | sed 's/\*//g' > "transposon_reference.list"
   GENE_BED_FILE="${MELT_DIR}/add_bed_files/Hg38/Hg38.genes.bed"
 elif [[ "$REF_VER" == "19" ]]; then
-  ls "${MELT_DIR}"/me_refs/1KGP_Hg19/*zip | sed 's/\*//g' > "${RUN_DIR}/transposon_reference.list"
+  ls "${MELT_DIR}"/me_refs/1KGP_Hg19/*zip | sed 's/\*//g' > "transposon_reference.list"
   GENE_BED_FILE="${MELT_DIR}/add_bed_files/1KGP_Hg19/hg19.genes.bed"
 fi
 
-##### Create output directory if it doesn't exist. then run MELT Single
-mkdir -p "${RUN_DIR}" && cd "${RUN_DIR}"
+##### Run MELT Single
 java -Xmx"${JVM_MAX_MEM}" \
   -jar "${MELT_DIR}/MELT.jar" \
   Single \
@@ -99,6 +95,6 @@ java -Xmx"${JVM_MAX_MEM}" \
   -r "${read_len}" \
   -e "${mean_is}" \
   -d "${MIN_CHR_LENGTH}" \
-  -t "${RUN_DIR}/transposon_reference.list" \
+  -t "transposon_reference.list" \
   -n "${GENE_BED_FILE}" \
-  -w "${RUN_DIR}"
+  -w "."

inputs/values/dockers.json

@@ -7,7 +7,7 @@
   "genomes_in_the_cloud_docker": "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.3.2-1510681135",
   "linux_docker": "marketplace.gcr.io/google/ubuntu1804",
   "manta_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/manta:2023-09-14-v0.28.3-beta-3f22f94d",
-  "melt_docker": "us.gcr.io/talkowski-sv-gnomad/melt:3159ce1",
+  "melt_docker": "us.gcr.io/talkowski-sv-gnomad/melt:a85c92f",
   "scramble_docker": "us.gcr.io/broad-dsde-methods/markw/scramble:mw-scramble-99af4c50",
   "samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2024-01-24-v0.28.4-beta-9debd6d7",

inputs/values/dockers_azure.json

@@ -7,7 +7,7 @@
   "genomes_in_the_cloud_docker": "vahid.azurecr.io/genomes-in-the-cloud:2.3.2-1510681135",
   "linux_docker": "vahid.azurecr.io/google/ubuntu1804",
   "manta_docker": "vahid.azurecr.io/gatk-sv/manta:2023-09-14-v0.28.3-beta-3f22f94d",
-  "melt_docker": "vahid.azurecr.io/melt:3159ce1",
+  "melt_docker": "vahid.azurecr.io/melt:a85c92f",
   "scramble_docker": "vahid.azurecr.io/scramble:mw-scramble-99af4c50",
   "samtools_cloud_docker": "vahid.azurecr.io/gatk-sv/samtools-cloud:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_docker": "vahid.azurecr.io/gatk-sv/sv-base:2024-01-24-v0.28.4-beta-9debd6d7",

wdl/MELT.wdl

@@ -511,24 +511,6 @@ task RunMELT {
     # these locations should be stable
     MELT_DIR="/MELT"
 
-    # `cromwell_root` and `cromwell-executions` are the **default**
-    # root directory for cromwell deployments on GCP and Azure respectively.
-    # The last option, i.e., $PWD, is the fall back option if the
-    # default root directory of the cromwell instance was changed,
-    # however, it is not a reliable option as it fails on GCP.
-    # It does not seem Cromwell sets a runtime environment variable
-    # exposing the configured value of the root directory,
-    # which could have provided a portable solution for this.
-    # The following solution works with the Cromwell deployments
-    # we are currently using on GCP and Azure.
-    if [ -d "/cromwell_root" ]; then
-      CROMWELL_ROOT="/cromwell_root"
-    elif [ -d "/cromwell-executions" ]; then
-      CROMWELL_ROOT="/cromwell-executions"
-    else
-      CROMWELL_ROOT="$PWD"
-    fi
-
     # these locations may vary based on MELT version number, so find them:
     MELT_ROOT=$(find "$MELT_DIR" -name "MELT.jar" | xargs -n1 dirname)
     MELT_SCRIPT=$(ls "$MELT_DIR/run_MELT"*.sh)
@@ -541,7 +523,6 @@ task RunMELT {
       ~{read_length} \
       ~{insert_size} \
       "$MELT_ROOT" \
-      "$CROMWELL_ROOT" \
       ~{reference_version}
 
     cat "~{melt_standard_vcf_header}" \