[TheiaProk] expose kleborate_virulence_score and kleborate_resistance…

…_score (#146) * expose kleborate_virulence_score and kleborate_resistance_score on theiaprok suit of workflows, and broad_terra_tools * update CI
theiagen · Aug 8, 2023 · a8d0e23 · a8d0e23
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commit a8d0e23
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Showing 8 changed files with 28 additions and 6 deletions.
diff --git a/tasks/utilities/task_broad_terra_tools.wdl b/tasks/utilities/task_broad_terra_tools.wdl
@@ -194,6 +194,8 @@ task export_taxon_tables {
     String? kleborate_otype
     String? kleborate_klocus_confidence
     String? kleborate_olocus_confidence
+    String? kleborate_virulence_score
+    String? kleborate_resistance_score
     File? kaptive_output_file_k
     File? kaptive_output_file_oc
     String? kaptive_version
@@ -508,6 +510,8 @@ task export_taxon_tables {
       "kleborate_otype": "~{kleborate_otype}",
       "kleborate_klocus_confidence": "~{kleborate_klocus_confidence}",
       "kleborate_olocus_confidence": "~{kleborate_olocus_confidence}",
+      "kleborate_virulence_score": "~{kleborate_virulence_score}",
+      "kleborate_resistance_score": "~{kleborate_resistance_score}",
       "ngmaster_tsv": "~{ngmaster_tsv}",
       "ngmaster_version": "~{ngmaster_version}",
       "ngmaster_ngmast_sequence_type": "~{ngmaster_ngmast_sequence_type}",

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -632,11 +632,11 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
       md5sum: 024971d1439dff7d59c0a26a824bd2c6
     - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
-      md5sum: f1bcb9e767ae3de776f6218e390bb166
+      md5sum: 499eb797a809306edf7e97005f67f8f2
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
-      md5sum: e98bdaa0c00d01b5e77859713ab91689
+      md5sum: a76d59109075ce8b861e63ffe70d7c77
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: ce89635c57ef1bd84a07af59948e80ea
+      md5sum: 53555c2f3e144e55f362080c5e75e434
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
       md5sum: 40d4e09a82030c8219b37f883cddaca4
     - path: miniwdl_run/workflow.log

diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -600,11 +600,11 @@
     - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
       md5sum: 024971d1439dff7d59c0a26a824bd2c6
     - path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
-      md5sum: f1bcb9e767ae3de776f6218e390bb166
+      md5sum: 499eb797a809306edf7e97005f67f8f2
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
-      md5sum: 17be58829cc4e6a1780cf227a2ec99ac
+      md5sum: c6ab2e13cf4802664b1c93e40a1cd5ba
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
-      md5sum: ce89635c57ef1bd84a07af59948e80ea
+      md5sum: 53555c2f3e144e55f362080c5e75e434
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
       md5sum: 53d322d895837c0bcb049786572e944d
     - path: miniwdl_run/workflow.log

diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl
@@ -270,6 +270,8 @@ workflow theiaprok_fasta {
         kleborate_otype = merlin_magic.kleborate_otype,
         kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence,
         kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence,
+        kleborate_virulence_score = merlin_magic.kleborate_virulence_score,
+        kleborate_resistance_score = merlin_magic.kleborate_resistance_score,
         ngmaster_tsv = merlin_magic.ngmaster_tsv,
         ngmaster_version = merlin_magic.ngmaster_version,
         ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type,
@@ -512,6 +514,8 @@ workflow theiaprok_fasta {
     String? kleborate_otype = merlin_magic.kleborate_otype
     String? kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence
     String? kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence
+    String? kleborate_virulence_score = merlin_magic.kleborate_virulence_score
+    String? kleborate_resistance_score = merlin_magic.kleborate_resistance_score
     # Neisseria gonorrhoeae Typing
     File? ngmaster_tsv = merlin_magic.ngmaster_tsv
     String? ngmaster_version = merlin_magic.ngmaster_version

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
@@ -395,6 +395,8 @@ workflow theiaprok_illumina_pe {
             kleborate_otype = merlin_magic.kleborate_otype,
             kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence,
             kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence,
+            kleborate_virulence_score = merlin_magic.kleborate_virulence_score,
+            kleborate_resistance_score = merlin_magic.kleborate_resistance_score,
             ngmaster_tsv = merlin_magic.ngmaster_tsv,
             ngmaster_version = merlin_magic.ngmaster_version,
             ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type,
@@ -747,6 +749,8 @@ workflow theiaprok_illumina_pe {
     String? kleborate_otype = merlin_magic.kleborate_otype
     String? kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence
     String? kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence
+    String? kleborate_virulence_score = merlin_magic.kleborate_virulence_score
+    String? kleborate_resistance_score = merlin_magic.kleborate_resistance_score
     # Neisseria gonorrhoeae Typing
     File? ngmaster_tsv = merlin_magic.ngmaster_tsv
     String? ngmaster_version = merlin_magic.ngmaster_version

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
@@ -365,6 +365,8 @@ workflow theiaprok_illumina_se {
             kleborate_otype = merlin_magic.kleborate_otype,
             kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence,
             kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence,
+            kleborate_virulence_score = merlin_magic.kleborate_virulence_score,
+            kleborate_resistance_score = merlin_magic.kleborate_resistance_score,
             ngmaster_tsv = merlin_magic.ngmaster_tsv,
             ngmaster_version = merlin_magic.ngmaster_version,
             ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type,
@@ -696,6 +698,8 @@ workflow theiaprok_illumina_se {
     String? kleborate_otype = merlin_magic.kleborate_otype
     String? kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence
     String? kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence
+    String? kleborate_virulence_score = merlin_magic.kleborate_virulence_score
+    String? kleborate_resistance_score = merlin_magic.kleborate_resistance_score
     # Neisseria gonorrhoeae Typing
     File? ngmaster_tsv = merlin_magic.ngmaster_tsv
     String? ngmaster_version = merlin_magic.ngmaster_version

diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl
@@ -352,6 +352,8 @@ workflow theiaprok_ont {
             kleborate_otype = merlin_magic.kleborate_otype,
             kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence,
             kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence,
+            kleborate_virulence_score = merlin_magic.kleborate_virulence_score,
+            kleborate_resistance_score = merlin_magic.kleborate_resistance_score,
             ngmaster_tsv = merlin_magic.ngmaster_tsv,
             ngmaster_version = merlin_magic.ngmaster_version,
             ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type,
@@ -653,6 +655,8 @@ workflow theiaprok_ont {
     String? kleborate_otype = merlin_magic.kleborate_otype
     String? kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence
     String? kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence
+    String? kleborate_virulence_score = merlin_magic.kleborate_virulence_score
+    String? kleborate_resistance_score = merlin_magic.kleborate_resistance_score
     # Neisseria gonorrhoeae Typing
     File? ngmaster_tsv = merlin_magic.ngmaster_tsv
     String? ngmaster_version = merlin_magic.ngmaster_version

diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
@@ -518,6 +518,8 @@ workflow merlin_magic {
     String? kleborate_otype = kleborate.kleborate_otype
     String? kleborate_klocus_confidence = kleborate.kleborate_klocus_confidence
     String? kleborate_olocus_confidence = kleborate.kleborate_olocus_confidence
+    String? kleborate_virulence_score = kleborate.kleborate_virulence_score
+    String? kleborate_resistance_score = kleborate.kleborate_resistance_score
     # Neisseria gonorrhoeae Typing
     File? ngmaster_tsv = ngmaster.ngmaster_tsv
     String? ngmaster_version = ngmaster.ngmaster_version