fix in get_columns_for_import.py (column -> col)

broadinstitute · Jul 12, 2023 · d628a8e · d628a8e
1 parent 2a0bf3b
commit d628a8e
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Showing 11 changed files with 23 additions and 23 deletions.
diff --git a/scripts/variantstore/wdl/GvsBulkIngestGenomes.wdl b/scripts/variantstore/wdl/GvsBulkIngestGenomes.wdl
@@ -165,7 +165,7 @@ task GetWorkspaceName {
 
     >>>
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         memory: "3 GB"
         disks: "local-disk 10 HDD"
         cpu: 1
@@ -213,7 +213,7 @@ task GetColumnNames {
     >>>
 
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         memory: "3 GB"
         disks: "local-disk 10 HDD"
         cpu: 1
@@ -242,7 +242,7 @@ task SplitBulkImportFofn {
     >>>
 
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         memory: "3 GB"
         disks: "local-disk 200 HDD"
         cpu: 1
@@ -293,7 +293,7 @@ task GenerateImportFofnFromDataTable {
             --error-file-name ~{error_file_name}
     >>>
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         memory: "3 GB"
         disks: "local-disk 200 HDD"
         cpu: 1

diff --git a/scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl b/scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl
@@ -261,7 +261,7 @@ task Add_AS_MAX_VQS_SCORE_ToVcf {
     File input_vcf
     String output_basename
 
-    String docker = "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+    String docker = "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
     Int cpu = 1
     Int memory_mb = 3500
     Int disk_size_gb = ceil(2*size(input_vcf, "GiB")) + 50

diff --git a/scripts/variantstore/wdl/GvsCallsetCost.wdl b/scripts/variantstore/wdl/GvsCallsetCost.wdl
@@ -62,7 +62,7 @@ task WorkflowComputeCosts {
     >>>
 
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
     }
 
     output {

diff --git a/scripts/variantstore/wdl/GvsCreateVATfromVDS.wdl b/scripts/variantstore/wdl/GvsCreateVATfromVDS.wdl
@@ -167,7 +167,7 @@ task MakeSubpopulationFilesAndReadSchemaFiles {
     # ------------------------------------------------
     # Runtime settings:
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         memory: "1 GB"
         preemptible: 3
         cpu: "1"
@@ -212,7 +212,7 @@ task StripCustomAnnotationsFromSitesOnlyVCF {
     # ------------------------------------------------
     # Runtime settings:
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         memory: "7 GiB"
         cpu: "2"
         preemptible: 3
@@ -297,7 +297,7 @@ task RemoveDuplicatesFromSitesOnlyVCF {
     # ------------------------------------------------
     # Runtime settings:
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         maxRetries: 3
         memory: "16 GB"
         preemptible: 3
@@ -457,7 +457,7 @@ task PrepVtAnnotationJson {
     # ------------------------------------------------
     # Runtime settings:
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         memory: "7 GB"
         preemptible: 3
         cpu: "1"
@@ -503,7 +503,7 @@ task PrepGenesAnnotationJson {
     # ------------------------------------------------
     # Runtime settings:
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         memory: "7 GB"
         preemptible: 3
         cpu: "1"

diff --git a/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl b/scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
@@ -177,7 +177,7 @@ task ExtractFromNonSuperpartitionedTables {
     }
 
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         disks: "local-disk 500 HDD"
     }
 }
@@ -244,7 +244,7 @@ task ExtractFromSuperpartitionedTables {
     }
 
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         disks: "local-disk 500 HDD"
     }
 }
@@ -312,7 +312,7 @@ task GenerateHailScripts {
         File hail_create_vat_inputs_script = 'hail_create_vat_inputs.py'
     }
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         disks: "local-disk 500 HDD"
     }
 }
diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl
@@ -339,7 +339,7 @@ task ProcessVCFHeaders {
   >>>
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
     disks: "local-disk 500 HDD"
   }
 }
@@ -510,7 +510,7 @@ task CurateInputLists {
                                              --vcf_index_list_file_name  ~{input_vcf_index_list}
   >>>
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
     memory: "3 GB"
     disks: "local-disk 100 HDD"
     bootDiskSizeGb: 15

diff --git a/scripts/variantstore/wdl/GvsPopulateAltAllele.wdl b/scripts/variantstore/wdl/GvsPopulateAltAllele.wdl
@@ -243,7 +243,7 @@ task PopulateAltAlleleTable {
     done
   >>>
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
     memory: "3 GB"
     disks: "local-disk 10 HDD"
     cpu: 1

diff --git a/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl b/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl
@@ -114,7 +114,7 @@ task PrepareRangesCallsetTask {
   }
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
     memory: "3 GB"
     disks: "local-disk 100 HDD"
     bootDiskSizeGb: 15

diff --git a/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl b/scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
@@ -19,7 +19,7 @@ task FilterIntervalListChromosomes {
             --output-interval-list "filtered.interval_list" --chromosome ~{sep=' --chromosome ' chromosomes}
     >>>
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
     }
     output {
         File out = "filtered.interval_list"

diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl
@@ -509,7 +509,7 @@ task ScaleXYBedValues {
     }
 
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
         maxRetries: 3
         memory: "7 GB"
         preemptible: 3
@@ -854,7 +854,7 @@ task SummarizeTaskMonitorLogs {
   # ------------------------------------------------
   # Runtime settings:
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-bf93ad833"
+    docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-07-12-alpine-0b2555b44"
     memory: "1 GB"
     preemptible: 3
     cpu: "1"

diff --git a/scripts/variantstore/wdl/extract/get_columns_for_import.py b/scripts/variantstore/wdl/extract/get_columns_for_import.py
@@ -243,13 +243,13 @@ def get_column_values(columnSamples, numSamples, user_defined_vcf, user_defined_
         # Check the contents of the columns: the duck algorithm.  If its contents LOOK like vcfs and indexes, go from there
         for col in path_ends_in_vcf_gz:
             # ...and has an analogue that looks like an index file?
-            index_column = f"{column}_index"
+            index_column = f"{col}_index"
             # is this the correct logic?  Or do we just want to look for ANY singular column that has contents that
             # look liks a vcf and ANY other singular column with contents that look like an index file?  Stick with
             # enforcing a naming convention for now...
             if index_column in path_ends_in_vcf_gz_tbi:
                 # woohoo!
-                final_vcf_column = column
+                final_vcf_column = col
                 final_vcf_index_column = index_column
                 found_vcf_column = True