added cli option for sample sheet generation

src/mikrokondo_tools/cli/__init__.py

@@ -6,6 +6,7 @@
 from mikrokondo_tools.__about__ import __version__
 from mikrokondo_tools.cli.download import download
 from mikrokondo_tools.cli.format import fmt
+from mikrokondo_tools.cli.samplesheet import samplesheet
 
 
 @click.group(context_settings={"help_option_names": ["-h", "--help"]}, invoke_without_command=True, no_args_is_help=True)
@@ -15,6 +16,7 @@ def mikrokondo_tools():
 
 mikrokondo_tools.add_command(fmt)
 mikrokondo_tools.add_command(download)
+mikrokondo_tools.add_command(samplesheet)
 
 
 

src/mikrokondo_tools/cli/samplesheet/__init__.py

@@ -0,0 +1,23 @@
+import click
+import pathlib as p
+import errno as e
+import sys
+
+from mikrokondo_tools.samplesheet import samplesheet as ss
+import mikrokondo_tools.utils as u
+
+@click.command(short_help="Generate a sample sheet for mikrokondo.", no_args_is_help=True)
+@click.option("-o", "--output-sheet", "output_sheet", required=True, type=click.Path(), help="The file to write your created output sheet to, this directory must already exist.")
+@click.option("-1", "--read-1-suffix", "read_1", type=click.STRING, help="A suffix to identify read 1", default="_R1_")
+@click.option("-2", "--read-2-suffix", "read_2", type=click.STRING, help="A suffix to identify read 2", default="_R2_")
+@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("sample_directory", type=click.Path(exists=True))
+def samplesheet(output_sheet, read_1, read_2, input_directory, schema_input):
+    logger = u.get_logger()
+    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)
+    return ngs_data.create_sample_sheet()