Added functionality for exclusion file

RIVM-bioinformatics · Jun 9, 2022 · 524857e · 524857e
1 parent 2172572
commit 524857e
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Showing 3 changed files with 13 additions and 1 deletion.
diff --git a/bin/python_scripts/collect_user_arguments.py b/bin/python_scripts/collect_user_arguments.py
@@ -90,6 +90,14 @@ def collect_arguments(self):
                 help = f"Full scientific name of the species sample, use underscores not spaces. If the species that you are looking for is not available choose 'other'. Options:{self.species_options}",
                 choices = self.species_options
             )
+            parser.add_argument(
+                '-ex',
+                '--exclusionfile',
+                type=pathlib.Path,
+                metavar='FILE',
+                dest="exclusion_file",
+                help='Path to the file that contains samplenames to be excluded.'  
+            )
             parser.add_argument(
                 "--resfinder_min_coverage",
                 type=float,

diff --git a/envs/juno_amr_master.yaml b/envs/juno_amr_master.yaml
@@ -18,4 +18,4 @@ dependencies:
   - pip:
     - PyYAML==5.3.1
     - tabulate==0.8.0
-    - "--editable=git+https://github.com/RIVM-bioinformatics/base_juno_pipeline.git@v0.2.6#egg=base_juno"
+    - "--editable=git+https://github.com/RIVM-bioinformatics/base_juno_pipeline.git@exclusion_file#egg=base_juno"
diff --git a/juno-amr.py b/juno-amr.py
@@ -24,6 +24,7 @@ def __init__(self,
                 input_dir,
                 output_dir,
                 species,
+                exclusion_file,
                 resfinder_min_coverage=0.6,
                 resfinder_identity_threshold=0.8,
                 db_dir = "/mnt/db/juno-amr",
@@ -71,6 +72,7 @@ def __init__(self,
 
         # Specific Juno-AMR pipeline attributes
         self.species = species
+        self.exclusion_file = exclusion_file
         self.resfinder_min_coverage=resfinder_min_coverage
         self.resfinder_identity_threshold= resfinder_identity_threshold
         self.run_pointfinder=run_pointfinder
@@ -98,6 +100,7 @@ def write_userparameters(self):
         config_params = {'input_dir': str(self.input_dir),
                         'output_dir': str(self.output_dir),
                         'species': str(self.species),
+                        'exclusion_file': str(self.exclusion_file),
                         'run_pointfinder': str(self.run_pointfinder),
                         'resfinder_min_coverage': self.resfinder_min_coverage,
                         'resfinder_identity_threshold': self.resfinder_identity_threshold,
@@ -128,6 +131,7 @@ def run_juno_amr_pipeline(self):
     JunoAmrRun(input_dir = args.input_dir, 
                     output_dir = args.output_dir, 
                     species=args.species,
+                    exclusion_file = args.exclusion_file,
                     run_pointfinder=args.run_pointfinder,
                     db_dir = args.db_dir,
                     resfinder_min_coverage = args.resfinder_min_coverage,