Merge pull request #360 from broadinstitute/dp-reporting

dashboard tsv should be txt

Author: dpark01

pipes/WDL/tasks/tasks_utils.wdl

@@ -351,7 +351,7 @@ task tsv_drop_cols {
     input {
         File          in_tsv
         Array[String] drop_cols
-        String        out_basename = basename(in_tsv, '.tsv') + ".drop"
+        String        out_filename = basename(in_tsv, '.tsv') + ".drop.tsv"
         String        docker = "quay.io/broadinstitute/py3-bio:0.1.2"
     }
     command <<<
@@ -363,7 +363,7 @@ task tsv_drop_cols {
         drop_cols = list(x for x in '~{sep="*" drop_cols}'.split('*') if x)
         if drop_cols:
             df.drop(columns=drop_cols, inplace=True)
-        df.to_csv("~{out_basename}.tsv", sep='\t', index=False)
+        df.to_csv("~{out_filename}", sep='\t', index=False)
         CODE
     >>>
     runtime {
@@ -374,7 +374,7 @@ task tsv_drop_cols {
         dx_instance_type: "mem1_ssd1_v2_x2"
     }
     output {
-        File out_tsv = "~{out_basename}.tsv"
+        File out_tsv = "~{out_filename}"
     }
 }
 

pipes/WDL/workflows/sarscov2_data_release.wdl

@@ -88,7 +88,7 @@ workflow sarscov2_data_release {
             input:
                 in_tsv = select_first([cdc_cumulative_metadata]),
                 drop_cols = ['internal_id','collaborator_id','matrix_id','hl7_message_id'],
-                out_basename = "metadata-cumulative"
+                out_filename = "metadata-cumulative.txt"
         }
         call terra.gcs_copy as dashboard_delivery {
             input: