From 71678c1ceb66ff03af787724afb1a7d1c3167806 Mon Sep 17 00:00:00 2001 From: VJalili Date: Wed, 10 Apr 2024 11:55:01 -0400 Subject: [PATCH 1/4] Make MELT scripts independent of the execution path. --- dockerfiles/melt/run_MELT_2.0.5.sh | 18 +++++++----------- wdl/MELT.wdl | 19 ------------------- 2 files changed, 7 insertions(+), 30 deletions(-) diff --git a/dockerfiles/melt/run_MELT_2.0.5.sh b/dockerfiles/melt/run_MELT_2.0.5.sh index f914c8ab6..16b0eaaca 100644 --- a/dockerfiles/melt/run_MELT_2.0.5.sh +++ b/dockerfiles/melt/run_MELT_2.0.5.sh @@ -19,7 +19,7 @@ set -euo pipefail ##### Usage statement usage(){ cat <10X) WGS data mapped with BWA. Positional arguments (all required): bam Full path to mapped bam file (bam.bai assumed accompanying the BAM) @@ -28,7 +28,6 @@ cat < "${RUN_DIR}/transposon_reference.list" + ls "${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}" 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}" \ No newline at end of file + -w "." diff --git a/wdl/MELT.wdl b/wdl/MELT.wdl index 350fd0c63..1e4207d49 100644 --- a/wdl/MELT.wdl +++ b/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}" \ From 6734cb20dfc216b7c62e071283cd57ed21fe8e7b Mon Sep 17 00:00:00 2001 From: VJalili Date: Thu, 11 Apr 2024 10:33:08 -0400 Subject: [PATCH 2/4] update a comment. --- dockerfiles/melt/run_MELT_2.0.5.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dockerfiles/melt/run_MELT_2.0.5.sh b/dockerfiles/melt/run_MELT_2.0.5.sh index 16b0eaaca..31962d626 100644 --- a/dockerfiles/melt/run_MELT_2.0.5.sh +++ b/dockerfiles/melt/run_MELT_2.0.5.sh @@ -85,7 +85,7 @@ elif [[ "$REF_VER" == "19" ]]; then GENE_BED_FILE="${MELT_DIR}/add_bed_files/1KGP_Hg19/hg19.genes.bed" fi -##### Create output directory if it doesn't exist. then run MELT Single +##### Run MELT Single java -Xmx"${JVM_MAX_MEM}" \ -jar "${MELT_DIR}/MELT.jar" \ Single \ From a85c92f85da24820c9fb3ab687ee2229970aa8d8 Mon Sep 17 00:00:00 2001 From: VJalili Date: Fri, 12 Apr 2024 10:18:29 -0400 Subject: [PATCH 3/4] Fix count. --- dockerfiles/melt/run_MELT_2.0.5.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dockerfiles/melt/run_MELT_2.0.5.sh b/dockerfiles/melt/run_MELT_2.0.5.sh index 31962d626..8042150dd 100644 --- a/dockerfiles/melt/run_MELT_2.0.5.sh +++ b/dockerfiles/melt/run_MELT_2.0.5.sh @@ -35,7 +35,7 @@ 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 From 25982d3cf528f686bf8dc6b96d6fb162b7e3e74c Mon Sep 17 00:00:00 2001 From: VJalili Date: Tue, 16 Apr 2024 10:09:31 -0400 Subject: [PATCH 4/4] tmp patch --- inputs/values/dockers.json | 2 +- inputs/values/dockers_azure.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json index d122f4322..e1cc7f4e5 100644 --- a/inputs/values/dockers.json +++ b/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", diff --git a/inputs/values/dockers_azure.json b/inputs/values/dockers_azure.json index ead09cb91..93e0bdbcb 100644 --- a/inputs/values/dockers_azure.json +++ b/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",