overhauling metagenomics subworkflow, the CLI wrapper, and the oneroof display

Author: nrminor

bin/__main__.py

@@ -148,7 +148,7 @@ def send_slack_notification(
         try:
             client = WebClient(token=slack_token)
             # Send the message to a channel
-            response = client.chat_postMessage(
+            client.chat_postMessage(
                 channel=user_id,  # or a user ID like "U12345678"
                 blocks=block,
             )

bin/slack_alerts.py

@@ -16,9 +16,6 @@
 from unittest.mock import Mock, mock_open, patch
 
 import pytest
-import yaml
-from paramiko.client import SSHClient
-
 from file_watcher import (
     Credentials,
     TransferRunner,
@@ -30,7 +27,7 @@
     try_access_env_setting,
     try_access_setting,
 )
-
+from paramiko.client import SSHClient
 
 # =============================================================================
 # Fixtures

bin/test_file_watcher.py

@@ -535,7 +535,7 @@ def test_malformed_file_handling(self, malformed_ivar_tsv, output_vcf_path):
 
     def test_strand_bias_detection(self, strand_bias_ivar_tsv, output_vcf_path):
         """Test strand bias detection."""
-        config = ConversionConfig(
+        ConversionConfig(
             file_in=strand_bias_ivar_tsv,
             file_out=output_vcf_path,
             ignore_strand_bias=False,

bin/test_ivar_variants_to_vcf.py

@@ -38,7 +38,7 @@ params {
     consensus             = params.ont_results + "/04_consensus_seqs"
 
     // metagenomic results 
-    metagenomics          = params.ont_results + "/metagenomics"
+    metagenomics          = params.ont_results + "/08_metagenomics"
 
     //haplyotyping results 
     haplotyping           = params.ont_results + "/haplotyping"