setting up snakemake workflow

Snakefile

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+# 2022 Benjamin J Perry
+# MIT License
+# Copyright (c) 2022 Benjamin J Perry
+# Version: 1.0
+# Maintainer: Benjamin J Perry
+# Email: [email protected]
+
+configfile: "config/config.yaml"
+
+import os
+
+onstart:
+    print(f"Working directory: {os.getcwd()}")
+    print("TOOLS: ")
+    os.system('echo "  bash: $(which bash)"')
+    os.system('echo "  PYTHON: $(which python)"')
+    os.system('echo "  CONDA: $(which conda)"')
+    os.system('echo "  SNAKEMAKE: $(which snakemake)"')
+    os.system('echo "  PYTHON VERSION: $(python --version)"')
+    os.system('echo "  CONDA VERSION: $(conda --version)"')
+    print(f"Env TMPDIR={os.environ.get('TMPDIR', '<n/a>')}")
+
+# Define samples from data directory using wildcards
+SAMPLES, = glob_wildcards('fastq/{samples}.fastq.gz')

config/config.yaml

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+# TMPDIR
+TMPDIR: /dataset/{Data Direcotry}/itmp #TODO: Update

fastq/README.md

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+# Location for fastq files