Remove VCF identifier input to PlotSVCountsPerSample for Terra (#224)

broadinstitute · Sep 3, 2021 · ca3b62c · ca3b62c
1 parent 4c0d89f
commit ca3b62c
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Showing 6 changed files with 9 additions and 16 deletions.
diff --git a/...ates/terra_workspaces/cohort_mode/workflow_configurations/PlotSVCountsPerSample.json.tmpl b/...ates/terra_workspaces/cohort_mode/workflow_configurations/PlotSVCountsPerSample.json.tmpl
@@ -4,6 +4,5 @@
   "PlotSVCountsPerSample.N_IQR_cutoff": "6",
 
   "PlotSVCountsPerSample.prefix": "${this.sample_set_id}",
-  "PlotSVCountsPerSample.vcfs" : "${[this.sites_filtered_manta_vcf, this.sites_filtered_delly_vcf, this.sites_filtered_wham_vcf, this.sites_filtered_melt_vcf, this.sites_filtered_depth_vcf]}",
-  "PlotSVCountsPerSample.vcf_identifiers" : "${this.algorithms_filtersites}"
+  "PlotSVCountsPerSample.vcfs" : "${[this.sites_filtered_manta_vcf, this.sites_filtered_delly_vcf, this.sites_filtered_wham_vcf, this.sites_filtered_melt_vcf, this.sites_filtered_depth_vcf]}"
 }
diff --git a/test_input_templates/FilterBatch/PlotSVCountsPerSample.json.tmpl b/test_input_templates/FilterBatch/PlotSVCountsPerSample.json.tmpl
@@ -9,6 +9,5 @@
     {{ test_batch.sites_filtered_wham_vcf | tojson }}, 
     {{ test_batch.sites_filtered_melt_vcf | tojson }}, 
     {{ test_batch.sites_filtered_depth_vcf | tojson }}
-  ],
-  "PlotSVCountsPerSample.vcf_identifiers" : ["manta", "wham", "melt", "depth"]
+  ]
 }
diff --git a/test_input_templates/FilterOutlierSamples/PlotSVCountsPerSample.json.tmpl b/test_input_templates/FilterOutlierSamples/PlotSVCountsPerSample.json.tmpl
@@ -6,6 +6,5 @@
   "PlotSVCountsPerSample.prefix": {{ test_batch.batch_name | tojson }},
   "PlotSVCountsPerSample.vcfs" : [ 
     {{ test_batch.baseline_final_vcf | tojson }}
-  ],
-  "PlotSVCountsPerSample.vcf_identifiers" : ["cohort_outlier_filtered"]
+  ]
 }
diff --git a/wdl/FilterBatch.wdl b/wdl/FilterBatch.wdl
@@ -69,7 +69,6 @@ workflow FilterBatch {
     input:
       prefix = batch,
       vcfs = [FilterBatchSites.sites_filtered_manta_vcf, FilterBatchSites.sites_filtered_delly_vcf, FilterBatchSites.sites_filtered_wham_vcf, FilterBatchSites.sites_filtered_melt_vcf, FilterBatchSites.sites_filtered_depth_vcf],
-      vcf_identifiers = FilterBatchSites.algorithms_filtersites,
       N_IQR_cutoff = outlier_cutoff_nIQR,
       sv_pipeline_docker = sv_pipeline_docker,
       runtime_attr_count_svs = runtime_attr_count_svs,

diff --git a/wdl/FilterBatchSites.wdl b/wdl/FilterBatchSites.wdl
@@ -67,7 +67,6 @@ workflow FilterBatchSites {
     File cutoffs = AdjudicateSV.cutoffs
     File scores = RewriteScores.updated_scores
     File RF_intermediate_files = AdjudicateSV.RF_intermediate_files
-    Array[String] algorithms_filtersites = algorithms
   }
 }
 

diff --git a/wdl/PlotSVCountsPerSample.wdl b/wdl/PlotSVCountsPerSample.wdl
@@ -7,22 +7,20 @@ workflow PlotSVCountsPerSample {
   input {
     String prefix
     Array[File?] vcfs  # in order of vcf_identifiers array. To skip one, use null keyword
-    Array[String] vcf_identifiers  # VCF identifiers - could be algorithms like manta, wham, etc or pesr, depth or just cohort VCF
     Int N_IQR_cutoff
     String sv_pipeline_docker
     RuntimeAttr? runtime_attr_count_svs
     RuntimeAttr? runtime_attr_plot_svcounts
     RuntimeAttr? runtime_attr_cat_outliers_preview
   }
 
-  Int num_identifiers = length(vcf_identifiers)
-
-  scatter (i in range(num_identifiers)) {
-    if (defined(vcfs[i])) {
+  scatter (vcf in vcfs) {
+    if (defined(vcf)) {
+      String vcf_name = basename(select_first([vcf]), ".vcf.gz")
       call CountSVsPerSamplePerType {
         input:
-          vcf = select_first([vcfs[i]]),
-          prefix = "~{prefix}.~{vcf_identifiers[i]}",
+          vcf = select_first([vcf]),
+          prefix = vcf_name,
           sv_pipeline_docker = sv_pipeline_docker,
           runtime_attr_override = runtime_attr_count_svs
       }
@@ -31,7 +29,7 @@ workflow PlotSVCountsPerSample {
         input:
           svcounts = CountSVsPerSamplePerType.sv_counts,
           n_iqr_cutoff = N_IQR_cutoff,
-          prefix = "~{prefix}.~{vcf_identifiers[i]}",
+          prefix = vcf_name,
           sv_pipeline_docker = sv_pipeline_docker,
           runtime_attr_override = runtime_attr_plot_svcounts
       }