Restore array output in gCNV WDLs for efficient postprocessing.

scripts/cnv_wdl/cnv_common_tasks.wdl

@@ -342,6 +342,10 @@ task PostprocessGermlineCNVCalls {
     String entity_id
     Array[File] gcnv_calls_tars
     Array[File] gcnv_model_tars
+    Array[File] calling_configs
+    Array[File] denoising_configs
+    Array[File] gcnvkernel_version
+    Array[File] sharded_interval_lists
     File contig_ploidy_calls_tar
     Array[String]? allosomal_contigs
     Int ref_copy_number_autosomal_contigs
@@ -370,13 +374,24 @@ task PostprocessGermlineCNVCalls {
         set -e
         export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}
 
+        sharded_interval_lists_array=(${sep=" " sharded_interval_lists})
+
         # untar calls to CALLS_0, CALLS_1, etc directories and build the command line
+        # also copy over shard config and interval files
         gcnv_calls_tar_array=(${sep=" " gcnv_calls_tars})
+        calling_configs_array=(${sep=" " calling_configs})
+        denoising_configs_array=(${sep=" " denoising_configs})
+        gcnvkernel_version_array=(${sep=" " gcnvkernel_version})
+        sharded_interval_lists_array=(${sep=" " sharded_interval_lists})
         calls_args=""
         for index in ${dollar}{!gcnv_calls_tar_array[@]}; do
             gcnv_calls_tar=${dollar}{gcnv_calls_tar_array[$index]}
-            mkdir CALLS_$index
-            tar xzf $gcnv_calls_tar -C CALLS_$index
+            mkdir -p CALLS_$index/SAMPLE_${sample_index}
+            tar xzf $gcnv_calls_tar -C CALLS_$index/SAMPLE_${sample_index}
+            cp ${dollar}{calling_configs_array[$index]} CALLS_$index/
+            cp ${dollar}{denoising_configs_array[$index]} CALLS_$index/
+            cp ${dollar}{gcnvkernel_version_array[$index]} CALLS_$index/
+            cp ${dollar}{sharded_interval_lists_array[$index]} CALLS_$index/
             calls_args="$calls_args --calls-shard-path CALLS_$index"
         done
 

scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl

@@ -187,7 +187,7 @@ workflow CNVGermlineCaseScatteredWorkflow {
         Array[Array[File]] read_counts_entity_id = CNVGermlineCaseWorkflow.read_counts_entity_id
         Array[Array[File]] read_counts = CNVGermlineCaseWorkflow.read_counts
         Array[File] contig_ploidy_calls_tars = CNVGermlineCaseWorkflow.contig_ploidy_calls_tar
-        Array[Array[File]] gcnv_calls_tars = CNVGermlineCaseWorkflow.gcnv_calls_tars
+        Array[Array[Array[File]]] gcnv_calls_tars = CNVGermlineCaseWorkflow.gcnv_calls_tars
         Array[Array[File]] gcnv_tracking_tars = CNVGermlineCaseWorkflow.gcnv_tracking_tars
         Array[Array[File]] genotyped_intervals_vcf = CNVGermlineCaseWorkflow.genotyped_intervals_vcf
         Array[Array[File]] genotyped_segments_vcf = CNVGermlineCaseWorkflow.genotyped_segments_vcf

scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl

@@ -211,12 +211,18 @@ workflow CNVGermlineCaseWorkflow {
         }
     }
 
+    Array[Array[File]] call_tars_sample_by_shard = transpose(GermlineCNVCallerCaseMode.gcnv_call_tars)
+
     scatter (sample_index in range(length(normal_bams))) {
         call CNVTasks.PostprocessGermlineCNVCalls {
             input:
                 entity_id = CollectCounts.entity_id[sample_index],
-                gcnv_calls_tars = GermlineCNVCallerCaseMode.gcnv_calls_tar,
+                gcnv_calls_tars = call_tars_sample_by_shard[sample_index],
                 gcnv_model_tars = gcnv_model_tars,
+                calling_configs = GermlineCNVCallerCaseMode.calling_config_json,
+                denoising_configs = GermlineCNVCallerCaseMode.denoising_config_json,
+                gcnvkernel_version = GermlineCNVCallerCaseMode.gcnvkernel_version_json,
+                sharded_interval_lists = GermlineCNVCallerCaseMode.sharded_interval_list,
                 allosomal_contigs = allosomal_contigs,
                 ref_copy_number_autosomal_contigs = ref_copy_number_autosomal_contigs,
                 contig_ploidy_calls_tar = DetermineGermlineContigPloidyCaseMode.contig_ploidy_calls_tar,
@@ -232,7 +238,7 @@ workflow CNVGermlineCaseWorkflow {
         Array[File] read_counts_entity_id = CollectCounts.entity_id
         Array[File] read_counts = CollectCounts.counts
         File contig_ploidy_calls_tar = DetermineGermlineContigPloidyCaseMode.contig_ploidy_calls_tar
-        Array[File] gcnv_calls_tars = GermlineCNVCallerCaseMode.gcnv_calls_tar
+        Array[Array[File]] gcnv_calls_tars = GermlineCNVCallerCaseMode.gcnv_call_tars
         Array[File] gcnv_tracking_tars = GermlineCNVCallerCaseMode.gcnv_tracking_tar
         Array[File] genotyped_intervals_vcf = PostprocessGermlineCNVCalls.genotyped_intervals_vcf
         Array[File] genotyped_segments_vcf = PostprocessGermlineCNVCalls.genotyped_segments_vcf
@@ -355,6 +361,9 @@ task GermlineCNVCallerCaseMode {
 
     # If optional output_dir not specified, use "out"
     String output_dir_ = select_first([output_dir, "out"])
+    Int num_samples = length(read_count_files)
+
+    String dollar = "$" #WDL workaround, see https://github.com/broadinstitute/cromwell/issues/1819
 
     command <<<
         set -e
@@ -406,8 +415,16 @@ task GermlineCNVCallerCaseMode {
             --caller-external-admixing-rate ${default="1.00" caller_external_admixing_rate} \
             --disable-annealing ${default="false" disable_annealing}
 
-        tar czf case-gcnv-calls-${scatter_index}.tar.gz -C ${output_dir_}/case-calls .
-        tar czf case-gcnv-tracking-${scatter_index}.tar.gz -C ${output_dir_}/case-tracking .
+        tar czf case-gcnv-tracking-shard-${scatter_index}.tar.gz -C ${output_dir_}/case-tracking .
+
+        CURRENT_SAMPLE=0
+        NUM_SAMPLES=${num_samples}
+        NUM_DIGITS=${dollar}{#NUM_SAMPLES}
+        while [ $CURRENT_SAMPLE -lt $NUM_SAMPLES ]; do
+            CURRENT_SAMPLE_WITH_LEADING_ZEROS=$(printf "%0${dollar}{NUM_DIGITS}d" $CURRENT_SAMPLE)
+            tar czf case-gcnv-calls-shard-${scatter_index}-sample-$CURRENT_SAMPLE_WITH_LEADING_ZEROS.tar.gz -C ${output_dir_}/case-calls/SAMPLE_$CURRENT_SAMPLE .
+            let CURRENT_SAMPLE=CURRENT_SAMPLE+1
+        done
     >>>
 
     runtime {
@@ -419,8 +436,8 @@ task GermlineCNVCallerCaseMode {
     }
 
     output {
-        File gcnv_calls_tar = "case-gcnv-calls-${scatter_index}.tar.gz"
-        File gcnv_tracking_tar = "case-gcnv-tracking-${scatter_index}.tar.gz"
+        Array[File] gcnv_call_tars = glob("case-gcnv-calls-shard-${scatter_index}-sample-*.tar.gz")
+        File gcnv_tracking_tar = "case-gcnv-tracking-shard-${scatter_index}.tar.gz"
         File calling_config_json = "${output_dir_}/case-calls/calling_config.json"
         File denoising_config_json = "${output_dir_}/case-calls/denoising_config.json"
         File gcnvkernel_version_json = "${output_dir_}/case-calls/gcnvkernel_version.json"

scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl

@@ -304,12 +304,18 @@ workflow CNVGermlineCohortWorkflow {
         }
     }
 
+    Array[Array[File]] call_tars_sample_by_shard = transpose(GermlineCNVCallerCohortMode.gcnv_call_tars)
+
     scatter (sample_index in range(length(CollectCounts.entity_id))) {
         call CNVTasks.PostprocessGermlineCNVCalls {
             input:
                 entity_id = CollectCounts.entity_id[sample_index],
-                gcnv_calls_tars = GermlineCNVCallerCohortMode.gcnv_calls_tar,
+                gcnv_calls_tars = call_tars_sample_by_shard[sample_index],
                 gcnv_model_tars = GermlineCNVCallerCohortMode.gcnv_model_tar,
+                calling_configs = GermlineCNVCallerCohortMode.calling_config_json,
+                denoising_configs = GermlineCNVCallerCohortMode.denoising_config_json,
+                gcnvkernel_version = GermlineCNVCallerCohortMode.gcnvkernel_version_json,
+                sharded_interval_lists = GermlineCNVCallerCohortMode.sharded_interval_list,
                 contig_ploidy_calls_tar = DetermineGermlineContigPloidyCohortMode.contig_ploidy_calls_tar,
                 allosomal_contigs = allosomal_contigs,
                 ref_copy_number_autosomal_contigs = ref_copy_number_autosomal_contigs,
@@ -329,7 +335,7 @@ workflow CNVGermlineCohortWorkflow {
         File contig_ploidy_model_tar = DetermineGermlineContigPloidyCohortMode.contig_ploidy_model_tar
         File contig_ploidy_calls_tar = DetermineGermlineContigPloidyCohortMode.contig_ploidy_calls_tar
         Array[File] gcnv_model_tars = GermlineCNVCallerCohortMode.gcnv_model_tar
-        Array[File] gcnv_calls_tars = GermlineCNVCallerCohortMode.gcnv_calls_tar
+        Array[Array[File]] gcnv_calls_tars = GermlineCNVCallerCohortMode.gcnv_call_tars
         Array[File] gcnv_tracking_tars = GermlineCNVCallerCohortMode.gcnv_tracking_tar
         Array[File] genotyped_intervals_vcfs = PostprocessGermlineCNVCalls.genotyped_intervals_vcf
         Array[File] genotyped_segments_vcfs = PostprocessGermlineCNVCalls.genotyped_segments_vcf
@@ -470,6 +476,9 @@ task GermlineCNVCallerCohortMode {
 
     # If optional output_dir not specified, use "out"
     String output_dir_ = select_first([output_dir, "out"])
+    Int num_samples = length(read_count_files)
+
+    String dollar = "$" #WDL workaround, see https://github.com/broadinstitute/cromwell/issues/1819
 
     command <<<
         set -e
@@ -529,9 +538,17 @@ task GermlineCNVCallerCohortMode {
             --caller-external-admixing-rate ${default="1.00" caller_external_admixing_rate} \
             --disable-annealing ${default="false" disable_annealing}
 
-        tar czf ${cohort_entity_id}-gcnv-model-${scatter_index}.tar.gz -C ${output_dir_}/${cohort_entity_id}-model .
-        tar czf ${cohort_entity_id}-gcnv-calls-${scatter_index}.tar.gz -C ${output_dir_}/${cohort_entity_id}-calls .
-        tar czf ${cohort_entity_id}-gcnv-tracking-${scatter_index}.tar.gz -C ${output_dir_}/${cohort_entity_id}-tracking .
+        tar czf ${cohort_entity_id}-gcnv-model-shard-${scatter_index}.tar.gz -C ${output_dir_}/${cohort_entity_id}-model .
+        tar czf ${cohort_entity_id}-gcnv-tracking-shard-${scatter_index}.tar.gz -C ${output_dir_}/${cohort_entity_id}-tracking .
+
+        CURRENT_SAMPLE=0
+        NUM_SAMPLES=${num_samples}
+        NUM_DIGITS=${dollar}{#NUM_SAMPLES}
+        while [ $CURRENT_SAMPLE -lt $NUM_SAMPLES ]; do
+            CURRENT_SAMPLE_WITH_LEADING_ZEROS=$(printf "%0${dollar}{NUM_DIGITS}d" $CURRENT_SAMPLE)
+            tar czf ${cohort_entity_id}-gcnv-calls-shard-${scatter_index}-sample-$CURRENT_SAMPLE_WITH_LEADING_ZEROS.tar.gz -C ${output_dir_}/${cohort_entity_id}-calls/SAMPLE_$CURRENT_SAMPLE .
+            let CURRENT_SAMPLE=CURRENT_SAMPLE+1
+        done
     >>>
 
     runtime {
@@ -543,9 +560,9 @@ task GermlineCNVCallerCohortMode {
     }
 
     output {
-        File gcnv_model_tar = "${cohort_entity_id}-gcnv-model-${scatter_index}.tar.gz"
-        File gcnv_calls_tar = "${cohort_entity_id}-gcnv-calls-${scatter_index}.tar.gz"
-        File gcnv_tracking_tar = "${cohort_entity_id}-gcnv-tracking-${scatter_index}.tar.gz"
+        File gcnv_model_tar = "${cohort_entity_id}-gcnv-model-shard-${scatter_index}.tar.gz"
+        Array[File] gcnv_call_tars = glob("${cohort_entity_id}-gcnv-calls-shard-${scatter_index}-sample-*.tar.gz")
+        File gcnv_tracking_tar = "${cohort_entity_id}-gcnv-tracking-shard-${scatter_index}.tar.gz"
         File calling_config_json = "${output_dir_}/${cohort_entity_id}-calls/calling_config.json"
         File denoising_config_json = "${output_dir_}/${cohort_entity_id}-calls/denoising_config.json"
         File gcnvkernel_version_json = "${output_dir_}/${cohort_entity_id}-calls/gcnvkernel_version.json"

src/main/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java

@@ -18,6 +18,7 @@
 import org.broadinstitute.hellbender.tools.copynumber.formats.metadata.LocatableMetadata;
 import org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig;
 import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
+import org.broadinstitute.hellbender.tools.copynumber.utils.CopyNumberUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
@@ -385,20 +386,20 @@ private boolean executeDeterminePloidyAndDepthPythonScript(final File samplesByC
                 : outputDir + File.separator;    //add trailing slash if necessary
         //note that the samples x coverage-by-contig table is referred to as "metadata" by gcnvkernel
         final List<String> arguments = new ArrayList<>(Arrays.asList(
-                "--sample_coverage_metadata=" + samplesByCoveragePerContigFile.getAbsolutePath(),
-                "--output_calls_path=" + outputDirArg + outputPrefix + CALLS_PATH_SUFFIX));
+                "--sample_coverage_metadata=" + CopyNumberUtils.getCanonicalPath(samplesByCoveragePerContigFile),
+                "--output_calls_path=" + CopyNumberUtils.getCanonicalPath(outputDirArg + outputPrefix + CALLS_PATH_SUFFIX)));
         arguments.addAll(germlineContigPloidyModelArgumentCollection.generatePythonArguments(runMode));
         arguments.addAll(germlineContigPloidyHybridADVIArgumentCollection.generatePythonArguments());
 
         final String script;
         if (runMode == RunMode.COHORT) {
             script = COHORT_DETERMINE_PLOIDY_AND_DEPTH_PYTHON_SCRIPT;
-            arguments.add("--interval_list=" + intervalsFile.getAbsolutePath());
-            arguments.add("--contig_ploidy_prior_table=" + inputContigPloidyPriorsFile.getAbsolutePath());
-            arguments.add("--output_model_path=" + outputDirArg + outputPrefix + MODEL_PATH_SUFFIX);
+            arguments.add("--interval_list=" + CopyNumberUtils.getCanonicalPath(intervalsFile));
+            arguments.add("--contig_ploidy_prior_table=" + CopyNumberUtils.getCanonicalPath(inputContigPloidyPriorsFile));
+            arguments.add("--output_model_path=" + CopyNumberUtils.getCanonicalPath(outputDirArg + outputPrefix + MODEL_PATH_SUFFIX));
         } else {
             script = CASE_DETERMINE_PLOIDY_AND_DEPTH_PYTHON_SCRIPT;
-            arguments.add("--input_model_path=" + inputModelDir);
+            arguments.add("--input_model_path=" + CopyNumberUtils.getCanonicalPath(inputModelDir));
         }
         return executor.executeScript(
                 new Resource(script, GermlineCNVCaller.class),

src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java

@@ -13,6 +13,7 @@
 import org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection;
 import org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleIntervalCollection;
 import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
+import org.broadinstitute.hellbender.tools.copynumber.utils.CopyNumberUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
@@ -406,21 +407,21 @@ private boolean executeGermlineCNVCallerPythonScript(final List<File> intervalSu
 
         //add required arguments
         final List<String> arguments = new ArrayList<>(Arrays.asList(
-                "--ploidy_calls_path=" + inputContigPloidyCallsDir,
-                "--output_calls_path=" + outputDirArg + outputPrefix + CALLS_PATH_SUFFIX,
-                "--output_tracking_path=" + outputDirArg + outputPrefix + TRACKING_PATH_SUFFIX));
+                "--ploidy_calls_path=" + CopyNumberUtils.getCanonicalPath(inputContigPloidyCallsDir),
+                "--output_calls_path=" + CopyNumberUtils.getCanonicalPath(outputDirArg + outputPrefix + CALLS_PATH_SUFFIX),
+                "--output_tracking_path=" + CopyNumberUtils.getCanonicalPath(outputDirArg + outputPrefix + TRACKING_PATH_SUFFIX)));
 
         //if a model path is given, add it to the argument (both COHORT and CASE modes)
         if (inputModelDir != null) {
-            arguments.add("--input_model_path=" + inputModelDir);
+            arguments.add("--input_model_path=" + CopyNumberUtils.getCanonicalPath(inputModelDir));
         }
 
         final String script;
         if (runMode == RunMode.COHORT) {
             script = COHORT_DENOISING_CALLING_PYTHON_SCRIPT;
             //these are the annotated intervals, if provided
-            arguments.add("--modeling_interval_list=" + specifiedIntervalsFile.getAbsolutePath());
-            arguments.add("--output_model_path=" + outputDirArg + outputPrefix + MODEL_PATH_SUFFIX);
+            arguments.add("--modeling_interval_list=" + CopyNumberUtils.getCanonicalPath(specifiedIntervalsFile));
+            arguments.add("--output_model_path=" + CopyNumberUtils.getCanonicalPath(outputDirArg + outputPrefix + MODEL_PATH_SUFFIX));
             if (inputAnnotatedIntervalsFile != null) {
                 arguments.add("--enable_explicit_gc_bias_modeling=True");
             } else {
@@ -432,7 +433,7 @@ private boolean executeGermlineCNVCallerPythonScript(final List<File> intervalSu
         }
 
         arguments.add("--read_count_tsv_files");
-        arguments.addAll(intervalSubsetReadCountFiles.stream().map(File::getAbsolutePath).collect(Collectors.toList()));
+        arguments.addAll(intervalSubsetReadCountFiles.stream().map(CopyNumberUtils::getCanonicalPath).collect(Collectors.toList()));
 
         arguments.addAll(germlineDenoisingModelArgumentCollection.generatePythonArguments(runMode));
         arguments.addAll(germlineCallingArgumentCollection.generatePythonArguments(runMode));

src/main/java/org/broadinstitute/hellbender/tools/copynumber/utils/CopyNumberUtils.java

@@ -0,0 +1,34 @@
+package org.broadinstitute.hellbender.tools.copynumber.utils;
+
+import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.utils.Utils;
+import org.broadinstitute.hellbender.utils.python.PythonScriptExecutor;
+
+import java.io.File;
+import java.io.IOException;
+
+public final class CopyNumberUtils {
+    private CopyNumberUtils() {}
+
+    /**
+     * File paths that are passed to {@link PythonScriptExecutor} must be canonical (rather than absolute).
+     * See https://github.com/broadinstitute/gatk/issues/4724.
+     */
+    public static String getCanonicalPath(final File file) {
+        Utils.nonNull(file);
+        try {
+            return file.getCanonicalPath();
+        } catch (final IOException e) {
+            throw new UserException.BadInput(String.format("Could not resolve a canonical file path: %s", file));
+        }
+    }
+
+    /**
+     * File paths that are passed to {@link PythonScriptExecutor} must be canonical (rather than absolute).
+     * See https://github.com/broadinstitute/gatk/issues/4724.
+     */
+    public static String getCanonicalPath(final String filename) {
+        Utils.nonEmpty(filename);
+        return getCanonicalPath(new File(filename));
+    }
+}