call_api task and update sarscov2_illumina_full with task

.dockstore.yml

@@ -270,3 +270,8 @@ workflows:
    primaryDescriptorPath: /pipes/WDL/workflows/trimal.wdl
    testParameterFiles:
     - empty.json
+ - name: update_data_tables
+   subclass: WDL
+   primaryDescriptorPath: /pipes/WDL/workflows/update_data_tables.wdl
+   testParameterFiles:
+    - empty.json

pipes/WDL/tasks/tasks_call_api.wdl

@@ -0,0 +1,36 @@
+version 1.0
+
+task  upload_entities_tsv{
+  input {
+    String        workspace_name
+    String        terra_project
+    File          tsv_file
+    Array[String] cleaned_reads_unaligned_bams_string
+    File          meta_by_filename_json
+
+    String        docker="schaluvadi/pathogen-genomic-surveillance:api-wdl"
+    Int?          machine_mem_gb
+  }
+
+  command {
+
+    echo ~{sep="," cleaned_reads_unaligned_bams_string} > cleaned_bam_strings.txt
+
+    python3 /projects/cdc-sabeti-covid-19/create_data_tables.py -t ~{tsv_file} \
+            -p ~{terra_project} \
+            -w ~{workspace_name} \
+            -b cleaned_bam_strings.txt \
+            -j ~{meta_by_filename_json}
+
+  }
+
+  runtime {
+    docker: docker
+    preemptible: 0
+    memory: select_first([machine_mem_gb, 10]) + " GB"
+  }
+
+  output {
+    String  status  = read_string(stdout())
+  }
+}

pipes/WDL/workflows/sarscov2_illumina_full.wdl

@@ -4,6 +4,7 @@ import "../tasks/tasks_read_utils.wdl" as read_utils
 import "../tasks/tasks_ncbi.wdl" as ncbi
 import "../tasks/tasks_nextstrain.wdl" as nextstrain
 import "../tasks/tasks_reports.wdl" as reports
+import "../tasks/tasks_call_api.wdl" as fapi_tables
 
 import "demux_deplete.wdl"
 import "assemble_refbased.wdl"
@@ -48,6 +49,9 @@ workflow sarscov2_illumina_full {
         String        sra_title
 
         Int           min_genome_bases = 15000
+
+        String        workspace_name
+        String        terra_project
     }
     Int     taxid = 2697049
     String  gisaid_prefix = 'hCoV-19/'
@@ -232,6 +236,16 @@ workflow sarscov2_illumina_full {
         out_name = "gisaid-meta-~{flowcell_id}.tsv"
     }
 
+    # create data tables with assembly_meta_tsv
+    call fapi_tables.upload_entities_tsv as data_tables {
+      input:
+        workspace_name = workspace_name,
+        terra_project = terra_project,
+        tsv_file = assembly_meta_tsv.combined,
+        cleaned_reads_unaligned_bams_string = demux_deplete.cleaned_reads_unaligned_bams,
+        meta_by_filename_json = demux_deplete.meta_by_filename_json
+    }
+
     output {
         Array[File] raw_reads_unaligned_bams     = demux_deplete.raw_reads_unaligned_bams
         Array[File] cleaned_reads_unaligned_bams = demux_deplete.cleaned_reads_unaligned_bams
@@ -280,5 +294,6 @@ workflow sarscov2_illumina_full {
         Int           num_submittable = length(select_all(submittable_id))
         Int           num_failed_annotation = length(select_all(failed_annotation_id))
         Int           num_samples = length(group_bams_by_sample.sample_names)
+        String        data_table_status = data_tables.status
     }
 }

pipes/WDL/workflows/update_data_tables.wdl

@@ -0,0 +1,28 @@
+version 1.0
+
+import "../tasks/tasks_call_api.wdl" as update_entities_api
+
+workflow update_data_tables {
+    meta {
+        description: "Create data tables in Terra workspace from provided tsv load file."
+        author: "Broad Viral Genomics"
+        email:  "[email protected]"
+    }
+
+    input {
+        String      workspace_name
+        String      terra_project
+        File        tsv_file
+    }
+
+    call update_entities_api.upload_entities_tsv as create_table {
+        input:
+            workspace_name = workspace_name,
+            terra_project = terra_project,
+            tsv_file = tsv_file
+    }
+
+    output {
+        String status_message = create_table.status
+    }
+}