From 583030f784268f0b4261b12d87c496582fe7d54a Mon Sep 17 00:00:00 2001 From: Ben Perry Date: Wed, 19 Oct 2022 14:24:37 +1300 Subject: [PATCH] setting up snakemake workflow --- Snakefile | 24 ++++++++++++++++++++++++ config/config.yaml | 2 ++ fastq/README.md | 1 + 3 files changed, 27 insertions(+) create mode 100644 Snakefile create mode 100644 config/config.yaml create mode 100644 fastq/README.md diff --git a/Snakefile b/Snakefile new file mode 100644 index 0000000..ed8d616 --- /dev/null +++ b/Snakefile @@ -0,0 +1,24 @@ +# 2022 Benjamin J Perry +# MIT License +# Copyright (c) 2022 Benjamin J Perry +# Version: 1.0 +# Maintainer: Benjamin J Perry +# Email: ben.perry@agresearch.co.nz + +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', '')}") + +# Define samples from data directory using wildcards +SAMPLES, = glob_wildcards('fastq/{samples}.fastq.gz') diff --git a/config/config.yaml b/config/config.yaml new file mode 100644 index 0000000..30b5ed8 --- /dev/null +++ b/config/config.yaml @@ -0,0 +1,2 @@ +# TMPDIR +TMPDIR: /dataset/{Data Direcotry}/itmp #TODO: Update diff --git a/fastq/README.md b/fastq/README.md new file mode 100644 index 0000000..837a609 --- /dev/null +++ b/fastq/README.md @@ -0,0 +1 @@ +# Location for fastq files \ No newline at end of file