Merge pull request #9 from DOED-DAAD/dev

Dev

src/mikrokondo_tools/cli/samplesheet/__init__.py

@@ -13,11 +13,12 @@
 @click.option("-s", "--schema-input", "schema_input", type=click.Path(), default=None, help="An optional schema_input.json file pre-downloaded for mikrokondo.")
 @click.argument("input_directory", type=click.Path(exists=True))
 def samplesheet(output_sheet, read_1, read_2, input_directory, schema_input):
-    logger = u.get_logger()
+    logger = u.get_logger(__name__)
+    output_sheet = p.Path(output_sheet)
     if output_sheet.is_file():
         logger.error("Input sample sheet already exists, please re-name your new sheet or the existing one. %s", output_sheet)
         sys.exit(e.EEXIST)
 
     data = ss.get_samples(p.Path(input_directory))
-    ngs_data = ss.NGSData(data[0], data[1], read_1, read_2, p.Path(output_sheet), schema_input)
+    ngs_data = ss.NGSData(data[0], data[1], read_1, read_2, output_sheet, schema_input)
     return ngs_data.create_sample_sheet()

src/mikrokondo_tools/samplesheet/samplesheet.py

@@ -193,9 +193,10 @@ def organize_data(self) -> t.Dict[str, t.List[SampleRow]]:
             sample_sheet[k] = []
             for idx in range(len(v[0])):
                 sample_sheet[k].append(SampleRow(sample=k, fastq_1=v[0][idx], fastq_2=v[1][idx]))
-
-        self.update_sample_sheet_se(sample_sheet, se_reads.items(), SampleRow.longreads_key())
-        self.update_sample_sheet_se(sample_sheet, assemblies.items(), SampleRow.assembly_key())
+        if se_reads:
+            self.update_sample_sheet_se(sample_sheet, se_reads.items(), SampleRow.longreads_key())
+        if assemblies:
+            self.update_sample_sheet_se(sample_sheet, assemblies.items(), SampleRow.assembly_key())
         return sample_sheet
 
     def update_sample_sheet_se(self, sample_sheet: t.Dict[str, t.List[SampleRow]], items: t.Iterable[t.Tuple[str, list]], field: str):