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VJaliliVJalili
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‎wdl/SVShell.wdl‎

Lines changed: 79 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -86,11 +86,19 @@ workflow SVShell {
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output {
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File test = RunSVShell.test
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File test2 = RunSVShell.test2
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# File final_vcf = RunSVShell.final_vcf
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# File pre_cleanup_vcf = RunSVShell.pre_cleanup_vcf
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# File stripy_json_output = RunSVShell.stripy_json_output
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# File metrics_file = RunSVShell.metrics_file
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# File ploidy_matrix = RunSVShell.ploidy_matrix
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File final_vcf = RunSVShell.final_vcf
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File final_vcf_idx = RunSVShell.final_vcf_idx
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File pre_cleanup_vcf = RunSVShell.pre_cleanup_vcf
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File pre_cleanup_vcf_idx = RunSVShell.pre_cleanup_vcf_idx
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File stripy_json_output = RunSVShell.stripy_json_output
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File stripy_tsv_output = RunSVShell.stripy_tsv_output
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File stripy_html_output = RunSVShell.stripy_html_output
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File stripy_vcf_output = RunSVShell.stripy_vcf_output
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File metrics_file = RunSVShell.metrics_file
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File qc_file = RunSVShell.qc_file
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File ploidy_matrix = RunSVShell.ploidy_matrix
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File ploidy_plots = RunSVShell.ploidy_plots
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File non_genotyped_unique_depth_calls = RunSVShell.non_genotyped_unique_depth_calls
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}
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}
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@@ -194,9 +202,24 @@ task RunSVShell {
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RuntimeAttr? runtime_attr_override
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}
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String final_vcf_filename = sample_id + ".gatk_sv.vcf.gz"
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String final_vcf_idx_filename = final_vcf_filename + ".tbi"
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String pre_cleanup_vcf_filename = batch + ".annotated.vcf.gz"
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String pre_cleanup_vcf_idx_filename = pre_cleanup_vcf_filename + ".tbi"
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String stripy_json_filename = sample_id + ".stripy.json"
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String stripy_tsv_filename = sample_id + ".stripy.tsv"
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String stripy_html_filename = sample_id + ".stripy.html"
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String stripy_vcf_filename = sample_id + ".stripy.vcf"
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String metrics_filename = "single_sample." + batch + ".metrics.tsv"
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String qc_filename = "sv_qc." + batch + ".tsv"
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String ploidy_matrix_filename = batch + "_ploidy_matrix.bed.gz"
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String ploidy_plots_filename = batch + "_ploidy_plots.tar.gz"
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String non_genotyped_unique_depth_calls_filename = batch + ".non_genotyped_unique_depth_calls.vcf.gz"
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command <<<
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set -Exeuo pipefail
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export BASE_DIR="${PWD}"
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export SV_SHELL_BASE_DIR="${PWD}/wd"
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export TMPDIR="${PWD}/wd/tmp"
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mkdir -p "${PWD}/wd/tmp"
@@ -297,33 +320,62 @@ task RunSVShell {
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echo "----------------------"
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echo "${PWD}"
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cp "${SV_SHELL_BASE_DIR}/single_sample_pipeline_inputs.json" .
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cp "${SV_SHELL_BASE_DIR}/single_sample_pipeline_outputs.json" .
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cp "${SV_SHELL_BASE_DIR}/single_sample_pipeline_inputs.json" "${BASE_DIR}/"
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cp "${SV_SHELL_BASE_DIR}/single_sample_pipeline_outputs.json" "${BASE_DIR}/"
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ls
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final_vcf=$(jq -r '.final_vcf' "${SV_SHELL_BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${final_vcf}" "${SV_SHELL_BASE_DIR}/final_vcf.vcf.gz"
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mv "${final_vcf}.tbi" "${SV_SHELL_BASE_DIR}/final_vcf.vcf.gz.tbi"
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final_vcf_path=$(jq -r '.final_vcf' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${final_vcf_path}" "${BASE_DIR}/~{final_vcf_filename}"
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mv "${final_vcf_path}.tbi" "${BASE_DIR}/~{final_vcf_idx_filename}"
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pre_cleanup_vcf_path=$(jq -r '.pre_cleanup_vcf' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${pre_cleanup_vcf_path}" "${BASE_DIR}/~{pre_cleanup_vcf_filename}"
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mv "${pre_cleanup_vcf_path}.tbi" "${BASE_DIR}/~{pre_cleanup_vcf_idx_filename}"
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stripy_json_path=$(jq -r '.stripy_json_output' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${stripy_json_path}" "${BASE_DIR}/~{stripy_json_filename}"
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stripy_tsv_path=$(jq -r '.stripy_tsv_output' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${stripy_tsv_path}" "${BASE_DIR}/~{stripy_tsv_filename}"
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stripy_html_path=$(jq -r '.stripy_html_output' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${stripy_html_path}" "${BASE_DIR}/~{stripy_html_filename}"
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stripy_vcf_path=$(jq -r '.stripy_vcf_output' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${stripy_vcf_path}" "${BASE_DIR}/~{stripy_vcf_filename}"
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metrics_path=$(jq -r '.metrics_file' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${metrics_path}" "${BASE_DIR}/~{metrics_filename}"
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qc_path=$(jq -r '.qc_file' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${qc_path}" "${BASE_DIR}/~{qc_filename}"
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ploidy_matrix_path=$(jq -r '.ploidy_matrix' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${ploidy_matrix_path}" "${BASE_DIR}/~{ploidy_matrix_filename}"
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ploidy_plots_path=$(jq -r '.ploidy_plots' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${ploidy_plots_path}" "${BASE_DIR}/~{ploidy_plots_filename}"
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non_genotyped_path=$(jq -r '.non_genotyped_unique_depth_calls' "${BASE_DIR}/single_sample_pipeline_outputs.json")
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mv "${non_genotyped_path}" "${BASE_DIR}/~{non_genotyped_unique_depth_calls_filename}"
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>>>
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output {
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File test = "single_sample_pipeline_inputs.json"
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File test2 = "single_sample_pipeline_outputs.json"
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# Map[String, String] manifest = read_json("pipeline_outputs_manifest.json")
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#
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File final_vcf = "final_vcf.vcf.gz"
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File final_vcf_idx = "final_vcf.vcf.gz.tbi"
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# File pre_cleanup_vcf = manifest["pre_cleanup_vcf"]
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# File stripy_json_output = manifest["stripy_json_output"]
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# File stripy_tsv_output = manifest["stripy_tsv_output"]
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# File stripy_html_output = manifest["stripy_html_output"]
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# File stripy_vcf_output = manifest["stripy_vcf_output"]
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# File metrics_file = manifest["metrics_file"]
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# File qc_file = manifest["qc_file"]
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# File ploidy_matrix = manifest["ploidy_matrix"]
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# File ploidy_plots = manifest["ploidy_plots"]
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# File non_genotyped_unique_depth_calls = manifest["non_genotyped_unique_depth_calls"]
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File inputs_json = "single_sample_pipeline_inputs.json"
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File outputs_json = "single_sample_pipeline_outputs.json"
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File final_vcf = final_vcf_filename
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File final_vcf_idx = final_vcf_idx_filename
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File pre_cleanup_vcf = pre_cleanup_vcf_filename
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File pre_cleanup_vcf_idx = pre_cleanup_vcf_idx_filename
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File stripy_json_output = stripy_json_filename
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File stripy_tsv_output = stripy_tsv_filename
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File stripy_html_output = stripy_html_filename
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File stripy_vcf_output = stripy_vcf_filename
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File metrics_file = metrics_filename
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File qc_file = qc_filename
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File ploidy_matrix = ploidy_matrix_filename
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File ploidy_plots = ploidy_plots_filename
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File non_genotyped_unique_depth_calls = non_genotyped_unique_depth_calls_filename
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}
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RuntimeAttr default_attr = object {
@@ -332,7 +384,7 @@ task RunSVShell {
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disk_gb: 500,
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boot_disk_gb: 30,
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preemptible_tries: 0,
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max_retries: 1
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max_retries: 0
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}
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RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
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