add basic test for new workflow

Author: adamcantor22

mmeds/config.py

@@ -294,7 +294,7 @@
     },
     "picrust2": {
         "parameters": [
-            "tables"  # this is going to always be 'asv_table.qza' TODO: default parameters?
+            "tables"  # this is going to always be 'asv_table.qza' and 'rep_seqs_table.qza'  TODO: default parameters?
         ],
         "optional_parameters": []
     }

mmeds/tests/unit/test_snakemake.py

@@ -6,6 +6,7 @@
 from mmeds.util import setup_environment
 from mmeds.logging import Logger
 
+
 class SnakemakeTests(TestCase):
     """ Test running snakemake analyses """
     @classmethod
@@ -36,13 +37,11 @@ def run_snakemake(self, path):
         run(f"rm -f {dag}; rm -f {rulegraph}; rm -f {snakefile}", shell=True)
         return 0
 
-
     def test_a_core_pipeline_taxonomic(self):
         """ Test snakemake standard pipeline analysis """
         result = self.run_snakemake(Path(fig.TEST_SNAKEMAKE_DIR) / "core_pipeline_taxonomic")
         self.assertEquals(result, 0)
 
-
     def test_b_lefse(self):
         """ Test snakemake lefse analysis """
         result = self.run_snakemake(Path(fig.TEST_SNAKEMAKE_DIR) / "lefse")
@@ -53,3 +52,8 @@ def test_c_lefse_failure(self):
         """ Test analysis with undefined snakemake method """
         result = self.run_snakemake(Path(fig.TEST_SNAKEMAKE_DIR) / "lefse_failure")
         self.assertEquals(result, 0)
+
+    def test_d_picrust2(self):
+        """ Test snakemake picrust2 analysis """
+        result = self.run_snakemake(Path(fig.TEST_SNAKEMAKE_DIR) / "picrust2")
+        self.assertEquals(result, 0)

test_files/test_snakemake/picrust2/picrust2.Snakefile

@@ -0,0 +1,11 @@
+configfile: "test_picrust2_config.yaml"
+report: "report.rst"
+
+include: "{snakemake_dir}/common.smk"
+include: "{snakemake_dir}/file_manipulation.smk"
+include: "{snakemake_dir}/table_filtering.smk"
+include: "{snakemake_dir}/functional_annotation.smk"
+
+rule results:
+    input:
+        directory("picrust2_out")

test_files/test_snakemake/picrust2/tables/asv_table.qza

@@ -0,0 +1,4 @@
+tables:
+  - asv_table
+  - rep_seqs_table
+