fix for nextclade parser taking no inputs

theiagen · Sep 21, 2023 · 03b6b88 · 03b6b88
1 parent 5eef197
commit 03b6b88
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Showing 2 changed files with 21 additions and 19 deletions.
diff --git a/tasks/utilities/task_theiacov_fasta_utilities.wdl b/tasks/utilities/task_theiacov_fasta_utilities.wdl
@@ -62,7 +62,7 @@ task create_dummy_file {
   Int disk_size = 10
   }
   command <<<
-    echo "This is the content of my file." > output.txt
+    echo "Untyped flu or nextclade not run for pathogen" > output.txt
   >>>
   output {
     File outputFile = "output.txt"

diff --git a/workflows/theiacov/wf_theiacov_fasta.wdl b/workflows/theiacov/wf_theiacov_fasta.wdl
@@ -43,21 +43,21 @@ workflow theiacov_fasta {
     String nextclade_rsv_a_tag = "2023-02-03T12:00:00Z"
     String nextclade_rsv_b_tag = "2023-02-03T12:00:00Z"
     # nextclade flu old inputs
-    String nextclade_flu_h1n1_ha_tag = "2023-04-02T12:00:00Z"
-    String nextclade_flu_h1n1_na_tag = "2023-04-02T12:00:00Z"
-    String nextclade_flu_h3n2_ha_tag = "2023-04-02T12:00:00Z"
-    String nextclade_flu_h3n2_na_tag = "2023-04-02T12:00:00Z"
-    String nextclade_flu_vic_ha_tag = "2023-04-02T12:00:00Z"
-    String nextclade_flu_vic_na_tag = "2023-04-02T12:00:00Z"
-    String nextclade_flu_yam_tag = "2022-07-27T12:00:00Z"
-    # nextclade flu inputs
-    #String nextclade_flu_h1n1_ha_tag = "2023-08-10T12:00:00Z"
-    #String nextclade_flu_h1n1_na_tag = "2023-08-10T12:00:00Z"
-    #String nextclade_flu_h3n2_ha_tag = "2023-08-10T12:00:00Z"
-    #String nextclade_flu_h3n2_na_tag = "2023-08-10T12:00:00Z"
-    #String nextclade_flu_vic_ha_tag = "2023-08-10T12:00:00Z"
-    #String nextclade_flu_vic_na_tag = "2023-08-10T12:00:00Z"
+    #String nextclade_flu_h1n1_ha_tag = "2023-04-02T12:00:00Z"
+    #String nextclade_flu_h1n1_na_tag = "2023-04-02T12:00:00Z"
+    #String nextclade_flu_h3n2_ha_tag = "2023-04-02T12:00:00Z"
+    #String nextclade_flu_h3n2_na_tag = "2023-04-02T12:00:00Z"
+    #String nextclade_flu_vic_ha_tag = "2023-04-02T12:00:00Z"
+    #String nextclade_flu_vic_na_tag = "2023-04-02T12:00:00Z"
     #String nextclade_flu_yam_tag = "2022-07-27T12:00:00Z"
+    # nextclade flu inputs
+    String nextclade_flu_h1n1_ha_tag = "2023-08-10T12:00:00Z"
+    String nextclade_flu_h1n1_na_tag = "2023-08-10T12:00:00Z"
+    String nextclade_flu_h3n2_ha_tag = "2023-08-10T12:00:00Z"
+    String nextclade_flu_h3n2_na_tag = "2023-08-10T12:00:00Z"
+    String nextclade_flu_vic_ha_tag = "2023-08-10T12:00:00Z"
+    String nextclade_flu_vic_na_tag = "2023-08-10T12:00:00Z"
+    String nextclade_flu_yam_tag = "2022-07-27T12:00:00Z"
     # sequencing values
     String seq_method
     String input_assembly_method
@@ -276,10 +276,12 @@ workflow theiacov_fasta {
   }
   # nextclade parser task
   if (organism == "sars-cov-2" || organism == "MPXV" || organism == "rsv_a" || organism == "rsv_b" || organism == "flu") {
-    call nextclade_task.nextclade_output_parser {
-      input:
-        nextclade_tsv = select_first([sarscov2_nextclade.nextclade_tsv, mpxv_nextclade.nextclade_tsv, rsv_a_nextclade.nextclade_tsv, rsv_b_nextclade.nextclade_tsv, flu_h1n1_ha_nextclade.nextclade_tsv, flu_h1n1_na_nextclade.nextclade_tsv, flu_h3n2_ha_nextclade.nextclade_tsv, flu_h3n2_na_nextclade.nextclade_tsv, flu_yam_ha_nextclade.nextclade_tsv, flu_vic_ha_nextclade.nextclade_tsv, flu_vic_na_nextclade.nextclade_tsv]),
-        organism = organism
+    if (defined(sarscov2_nextclade.nextclade_tsv) || defined(mpxv_nextclade.nextclade_tsv) || defined(rsv_a_nextclade.nextclade_tsv) || defined(rsv_b_nextclade.nextclade_tsv) || defined(flu_h1n1_ha_nextclade.nextclade_tsv) || defined(flu_h1n1_na_nextclade.nextclade_tsv) || defined(flu_h3n2_ha_nextclade.nextclade_tsv) || defined(flu_h3n2_na_nextclade.nextclade_tsv) || defined(flu_yam_ha_nextclade.nextclade_tsv) || defined(flu_vic_ha_nextclade.nextclade_tsv) || defined(flu_vic_na_nextclade.nextclade_tsv)) {
+      call nextclade_task.nextclade_output_parser {
+        input:
+          nextclade_tsv = select_first([sarscov2_nextclade.nextclade_tsv, mpxv_nextclade.nextclade_tsv, rsv_a_nextclade.nextclade_tsv, rsv_b_nextclade.nextclade_tsv, flu_h1n1_ha_nextclade.nextclade_tsv, flu_h1n1_na_nextclade.nextclade_tsv, flu_h3n2_ha_nextclade.nextclade_tsv, flu_h3n2_na_nextclade.nextclade_tsv, flu_yam_ha_nextclade.nextclade_tsv, flu_vic_ha_nextclade.nextclade_tsv, flu_vic_na_nextclade.nextclade_tsv]),
+          organism = organism
+      }
     }
   }
   # vadr task