Merge branch 'bug_fixes' into 'master'

Fix bugs in current master due to post_out switch See merge request algorithm/megalodon!80
nanoporetech · Oct 25, 2021 · 16a6060 · 16a6060
2 parents 9826116 + 5bc21b3
commit 16a6060
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/megalodon/backends.py b/megalodon/backends.py
@@ -208,9 +208,9 @@ def parse_backend_params(args, num_fast5_startup_reads=5):
             args.guppy_server_port = "auto"
         # only start server with post out if flip-flop mods or variants are
         # requested
-        post_out = (
-            mh.PR_MOD_NAME in args.outputs and args.remora_model is None
-        ) or mh.PR_VAR_NAME in args.outputs
+        post_out = hasattr(args, "outputs") and (
+            mh.PR_MOD_NAME in args.outputs or mh.PR_VAR_NAME in args.outputs
+        )
         pyguppy_params = PYGUPPY_PARAMS(
             available=True,
             config=args.guppy_config,

diff --git a/megalodon_extras/calibrate_generate_mod_stats_from_msf.py b/megalodon_extras/calibrate_generate_mod_stats_from_msf.py
@@ -377,6 +377,7 @@ def _main(args):
             + "guppy logs."
         )
     args = add_trim_guppy_none(args)
+    args.outputs = [mh.PR_MOD_NAME]
     # make edge_buffer >= context_bases to simplify processing
     if args.edge_buffer < args.mod_context_bases:
         LOGGER.warning(

diff --git a/megalodon_extras/calibrate_generate_variant_stats.py b/megalodon_extras/calibrate_generate_variant_stats.py
@@ -645,6 +645,7 @@ def _main(args):
     # this script.
     args.do_not_use_guppy_server = False
     args.output_directory = args.guppy_logs_output_directory
+    args.outputs = [mh.PR_VAR_NAME]
 
     LOGGER.info("Loading model.")
     backend_params = backends.parse_backend_params(args)