Remove last references to old denovo pipelines as part of #548.

cfe-lab · Mar 25, 2020 · 0bcfd06 · 0bcfd06
1 parent e46da43
commit 0bcfd06
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Showing 3 changed files with 1 addition and 20 deletions.
diff --git a/micall/monitor/kive_watcher.py b/micall/monitor/kive_watcher.py
@@ -462,13 +462,6 @@ def add_sample_group(self, base_calls, sample_group):
                                 direction + ' read from MiSeq run ' +
                                 folder_watcher.run_name)
                             sample_watcher.fastq_datasets.append(fastq_dataset)
-                    if (self.config.denovo_pipeline_id or
-                            self.config.denovo_combined_pipeline_id):
-                        sample_name = trim_name(fastq_name)
-                        name_dataset = self.find_or_upload_dataset(
-                            BytesIO(sample_name.encode('UTF8')),
-                            f'{sample_name}_name.txt')
-                        sample_watcher.name_datasets.append(name_dataset)
 
                 folder_watcher.sample_watchers.append(sample_watcher)
                 return sample_watcher

diff --git a/micall/monitor/sample_watcher.py b/micall/monitor/sample_watcher.py
@@ -101,9 +101,7 @@ def active_run_count(self):
                     for pipeline_id in (
                         self.runner.config.micall_main_pipeline_id,
                         self.runner.config.denovo_main_pipeline_id,
-                        self.runner.config.mixed_hcv_pipeline_id,
-                        self.runner.config.denovo_pipeline_id,
-                        self.runner.config.denovo_combined_pipeline_id))
+                        self.runner.config.mixed_hcv_pipeline_id))
 
             all_samples = set(self.all_samples)
             return n * len(all_samples - self.completed_samples)

diff --git a/micall_watcher.py b/micall_watcher.py
@@ -40,16 +40,6 @@ def parse_args(argv=None):
         type=int,
         default=os.environ.get('MICALL_MIXED_HCV_PIPELINE_ID', None),
         help="id of Mixed HCV pipeline's container app")
-    parser.add_argument(
-        '--denovo_pipeline_id',
-        type=int,
-        default=os.environ.get('MICALL_DENOVO_PIPELINE_ID', None),
-        help="id of Denovo pipeline's container app")
-    parser.add_argument(
-        '--denovo_combined_pipeline_id',
-        type=int,
-        default=os.environ.get('MICALL_DENOVO_COMBINED_PIPELINE_ID', None),
-        help="id of Denovo pipeline's container app for combining two samples")
     parser.add_argument(
         '--denovo_main_pipeline_id',
         type=int,