Merge pull request #259 from cov-lineages/dev

Add security features to use of scorpio
cov-lineages · Jun 24, 2021 · 0f6edad · 0f6edad
2 parents e2c9c51 + 54ffa79
commit 0f6edad
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Showing 2 changed files with 6 additions and 9 deletions.
diff --git a/pangolin/__init__.py b/pangolin/__init__.py
@@ -1,5 +1,6 @@
 _program = "pangolin"
-__version__ = "3.1.4"
+__version__ = "3.1.5"
+
 
 __all__ = ["pangolearn",
     "utils"]

diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk
@@ -175,6 +175,8 @@ rule scorpio:
         -i {input.fasta:q} \
         -o {output.report:q} \
         -t {workflow.cores} \
+        --output-counts \
+        --pangolin \
         --long &> {log:q}
         """
 
@@ -219,10 +221,7 @@ rule generate_report:
                         new_row["scorpio_conflict"] = scorpio_call_info["conflict"]
                         new_row["note"] = f'scorpio call: Alt alleles {scorpio_call_info["alt_count"]}; Ref alleles {scorpio_call_info["ref_count"]}; Amb alleles {scorpio_call_info["ambig_count"]}'
 
-                        if "(" in new_row["scorpio_call"]:
-                            scorpio_lineage = new_row["scorpio_call"].split("(")[1].split("+")[0].split("-like")[0]
-                        else:
-                            scorpio_lineage = new_row["scorpio_call"].split("+")[0].split("-like")[0]
+                        scorpio_lineage = scorpio_call_info["mrca_lineage"]
                         expanded_scorpio_lineage = expand_alias(scorpio_lineage, alias_dict)
                         expanded_pango_lineage = expand_alias(row['lineage'], alias_dict)
                         if '/' not in scorpio_lineage:
@@ -346,10 +345,7 @@ rule usher_to_report:
                         scorpio_conflict = scorpio_call_info["conflict"]
                         note = f'scorpio call: Alt alleles {scorpio_call_info["alt_count"]}; Ref alleles {scorpio_call_info["ref_count"]}; Amb alleles {scorpio_call_info["ambig_count"]}'
 
-                        if "(" in scorpio_call:
-                            scorpio_lineage = scorpio_call.split("(")[1].split("+")[0].split("-like")[0]
-                        else:
-                            scorpio_lineage = scorpio_call.split("+")[0].split("-like")[0]
+                        scorpio_lineage = scorpio_call_info["mrca_lineage"]
                         expanded_scorpio_lineage = expand_alias(scorpio_lineage, alias_dict)
                         expanded_pango_lineage = expand_alias(lineage, alias_dict)
                         if expanded_scorpio_lineage and expanded_pango_lineage and not expanded_pango_lineage.startswith(expanded_scorpio_lineage):