workflow: don't use metadata for sc2rf_recombinants when exclude_nega…

…tives is true

sc2rf/postprocess.py

@@ -813,6 +813,12 @@ def main(
 
     if nextclade and nextclade_auto_pass:
 
+        logger.info(
+            "Auto-passing lineages through sc2rf: {}".format(
+                ",".join(nextclade_auto_pass_lineages)
+            )
+        )
+
         # Identify negative samples to auto-pass
         auto_pass_df = nextclade_df[
             (nextclade_df["Nextclade_pango"] != NO_DATA_CHAR)
@@ -860,7 +866,9 @@ def main(
 
     # ---------------------------------------------------------------------
     # Write exclude strains (false positives)
+
     outpath_exclude = os.path.join(outdir, prefix + ".exclude.tsv")
+    logger.info("Writing strains to exclude: {}".format(outpath_exclude))
     if len(false_positives) > 0:
         with open(outpath_exclude, "w") as outfile:
             for strain, reason in false_positives.items():
@@ -889,6 +897,7 @@ def main(
     # write output table
 
     # Drop old columns, if there were only negative samples, these columns don't exist
+    logger.info("Formatting output columns.")
     if set(df["sc2rf_status"]) != set(["negative"]):
         df.drop(
             [

workflow/Snakefile

@@ -597,6 +597,12 @@ def _params_sc2rf_recombinants(build):
   if auto_pass: params["auto_pass"] = "--nextclade-auto-pass {}".format(",".join(auto_pass))
   else: params["auto_pass"] = ""
 
+  # The metadata param will not be used if we are excluding negatives
+  metadata = _inputs(build)["metadata"]
+  exclude_negatives = config["builds"][build]["sc2rf"]["exclude_negatives"]
+  if not exclude_negatives: params["metadata"] = "--metadata {}".format(metadata)
+  else: params["metadata"] = ""
+
   return params
 
 
@@ -636,6 +642,7 @@ rule sc2rf_recombinants:
     max_breakpoints = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["max_breakpoints"],
     motifs          = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["motifs"],
     auto_pass       = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["auto_pass"],
+    metadata        = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["metadata"],
     # Join inputs together with commas
     ansi            = lambda wildcards: ",".join(_inputs_sc2rf_recombinants(wildcards.build)["ansi"]),
     csv             = lambda wildcards: ",".join(_inputs_sc2rf_recombinants(wildcards.build)["csv"]),
@@ -658,7 +665,7 @@ rule sc2rf_recombinants:
       --nextclade {input.nextclade} \
       --nextclade-no-recomb {input.nextclade_no_recomb} \
       --lineage-tree {input.lineage_tree} \
-      --metadata {input.metadata} \
+      {params.metadata} \
       {params.auto_pass} \
       {params.motifs} \
       {params.min_len} \