Ali Khan akhanf

Associate Prof at Robarts Research Institute, Western University

akhanf / Snakefile

Created May 21, 2020 12:42

Sample Snakefile for MDT

	from os.path import join

	configfile: 'config.yml'

	container: config['container']


	rule create_protocol:
	input:
	bvec = join(config['in_dir'],config['bvec']),

akhanf / snakemake_iterative_template

Last active October 2, 2020 23:52

Example of recipe for iteratively building a template using recursion (view graph with: snakemake -np --dag | dot | display)


	input_images = ['A','B','C']
	shell('touch {input_images}')

	max_iters = 4

	#need this to make sure iterations don't go below 0!
	wildcard_constraints:
	iteration="[0-9]+"

akhanf / snakemake_remotebatch

Created April 21, 2020 13:06

batch submission script

	#!/bin/bash

	hours=6
	mem=128000
	gpus=1
	cpus=32

	if [ "$#" -lt 2 ]
	then
	echo "Usage $0 RULE_NAME NUM_BATCHES <optional snakemake args>"