make standalone sarscov2_sequencing_reports workflow accept multiple …

…runs of input
broadinstitute · Mar 25, 2021 · 5bf1ead · 5bf1ead
1 parent 1a2c8f9
commit 5bf1ead
Showing 1 changed file with 22 additions and 3 deletions.
diff --git a/pipes/WDL/workflows/sarscov2_sequencing_reports.wdl b/pipes/WDL/workflows/sarscov2_sequencing_reports.wdl
@@ -1,16 +1,35 @@
 version 1.0
 
 import "../tasks/tasks_sarscov2.wdl" as sarscov2
+import "../tasks/tasks_reports.wdl" as reports
 
 workflow sarscov2_sequencing_reports {
     meta {
         description: "Produce per-state and per-collaborator weekly reports of SARS-CoV-2 surveillance data."
     }
 
-    call sarscov2.sequencing_report 
+    input {
+        Array[File] assembly_stats_tsvs
+        String      max_date
+    }
+
+    call reports.tsv_join {
+        input:
+            input_tsvs = assembly_stats_tsvs,
+            id_col = 'sample',
+            out_basename = 'assembly_stats-cumulative-~{max_date}'
+    }
+
+    call sarscov2.sequencing_report {
+        input:
+            assembly_stats_tsv = tsv_join.out_tsv,
+            max_date = max_date
+    }
 
     output {
-        Array[File]  sequencing_reports_pdfs  = sequencing_report.reports
-        Array[File]  sequencing_reports_xlsxs = sequencing_report.sheets
+        File         assembly_stats_cumulative_tsv = tsv_join.out_tsv
+        Array[File]  sequencing_reports_pdfs       = sequencing_report.reports
+        Array[File]  sequencing_reports_xlsxs      = sequencing_report.sheets
+        File         sequencing_reports_zip        = sequencing_report.all_zip
     }
 }