Makes use of autoBIGS 0.14.* and fixes CSV export issue caused by missing target.

Jenkinsfile

@@ -37,10 +37,6 @@ pipeline {
         stage("publish") {
             parallel {
                 stage ("git.reslate.systems") {
-                    when {
-                        branch '**/main'
-                    }
-
                     environment {
                         CREDS = credentials('username-password-rs-git')
                     }

pyproject.toml

@@ -8,7 +8,7 @@ dynamic = ["version"]
 readme = "README.md"
 license = {text = "GPL-3.0-or-later"}
 dependencies = [
-    "autoBIGS-engine==0.13.*"
+    "autoBIGS-engine==0.14.*"
 ]
 requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."

src/autobigs/cli/info.py

@@ -53,6 +53,7 @@ async def run(args: Namespace):
                     writer.writerows(sorted_seqdef_dbs)
                     print("\nDatabase output written to {0}".format(args.csv_output))
 
+        if args.list_bigsdb_schemes:
             csv_scheme_rows = []
             for bigsdb_scheme_name in args.list_bigsdb_schemes:
                 schemes = await bigsdb_index.get_schemes_for_seqdefdb(bigsdb_scheme_name)

src/autobigs/cli/st.py

@@ -79,7 +79,7 @@ async def run(args: Namespace):
             if not isinstance(mlst_profiler, BIGSdbMLSTProfiler):
                 raise TypeError("MLST profiler type invalid")
             mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, args.stop_on_fail)
-            failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
+            failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out, await bigsdb_index.get_scheme_loci(args.seqdefdb, selected_scheme_id))
             if len(failed) > 0:
                 print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}")
             print(f"Completed fetching from {args.seqdefdb} for {scheme_name_lookup[selected_scheme_id]}s for {len(fastas)} sequences.")