theiacov_fasta wf logic change for flu (#305)

* theiacov_fasta wf logic change. only run abricate if user sets organism to "flu" AND flu_subtype is not set or unknown

* allow for empty string to be passed into organism_parameters subwf for flu_subtype input string

* instead of empty string, pass "N/A" for when flu_subtype is unknown or undefined by user

* force theiacov_fasta CI to skip pangolin due to errors with really long pathnames when scorpio is running

* update the CI correctly this time. booleans are special

* update hashes for pangolin command and output CSV (expected changes)

tests/inputs/theiacov/wf_theiacov_fasta.json

@@ -3,5 +3,6 @@
     "theiacov_fasta.assembly_fasta": "tests/data/theiacov/fasta/clearlabs.fasta.gz",
     "theiacov_fasta.seq_method": "clearlabs",
     "theiacov_fasta.input_assembly_method": "clearlabs",
-    "theiacov_fasta.reference_genome": "tests/inputs/completely-empty-for-test.txt"
+    "theiacov_fasta.reference_genome": "tests/inputs/completely-empty-for-test.txt",
+    "theiacov_fasta.pangolin4.skip_scorpio": true
 }

tests/workflows/theiacov/test_wf_theiacov_fasta.yml

@@ -122,7 +122,7 @@
     - path: miniwdl_run/call-nextclade_output_parser/work/input.tsv
       md5sum: 9b459df2831ab1974c9c8cef5bc5340e
     - path: miniwdl_run/call-pangolin4/command
-      md5sum: 85d3001929bde4169a11947fb38fb693
+      md5sum: 558f8f3b23b7562e7dca67dc0a647522
     - path: miniwdl_run/call-pangolin4/inputs.json
     - path: miniwdl_run/call-pangolin4/outputs.json
     - path: miniwdl_run/call-pangolin4/stderr.txt
@@ -144,7 +144,7 @@
       md5sum: 9f9c4c00a1ceb5526bed7dc4cdb3dcfd
     - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/clearlabs.fasta.gz
     - path: miniwdl_run/call-pangolin4/work/fasta.pangolin_report.csv
-      md5sum: 81679363ffed582650f8512794035806
+      md5sum: c8ddc2706b30b5bfcaf32636ed5a63ec
     - path: miniwdl_run/call-vadr/command
       md5sum: f4ad614b7ad39f28a8145cec280a93c0
     - path: miniwdl_run/call-vadr/inputs.json

workflows/theiacov/wf_theiacov_fasta.wdl

@@ -37,7 +37,8 @@ workflow theiacov_fasta {
     Int? maxlen
     String? vadr_opts
   }
-  if (!defined(flu_subtype)) {
+  # only run abricate if user sets organism = "flu" AND if flu_subtype is unknown/not set by user
+  if (!defined(flu_subtype) && organism == "flu") {
     call abricate.abricate_flu {
       input:
         assembly = assembly_fasta,
@@ -49,7 +50,7 @@ workflow theiacov_fasta {
     input:
       organism = organism,
       flu_segment = flu_segment,
-      flu_subtype = select_first([flu_subtype, abricate_subtype]),
+      flu_subtype = select_first([flu_subtype, abricate_subtype, "N/A"]),
       reference_genome = reference_genome,
       genome_length = genome_length,
       nextclade_ds_reference = nextclade_dataset_reference,