example_snakefile

import shutil

configfile:
	"example_config.yaml"
print(config['data'])

if config['gzipped_reads'] == "True":
	gz=".gz"
if config['gzipped_reads'] == "False":
	gz=""

if config['paired_reads'] == "True":
	SAMPLES, = glob_wildcards(config['data']+"/{id}_R1.fastq"+gz)
if config['paired_reads'] == "False":
	SAMPLES, = glob_wildcards(config['data']+"/{id}.fastq"+gz)

#SAMPLES, = glob_wildcards(config['data']+"/{id}_R1.fastq"+gz)
print(SAMPLES)

RESULTS = config['results_loc']
print(RESULTS)

onstart:
	print("The samples used in this analysis are:"),
	print(SAMPLES),
	print("Running the differential gene expression (DGE) pipeline") 

rule all:
	input:
		expand(config['results_loc'] + "/results/fastq_trimmed/{sample}.html", sample=SAMPLES),
		expand(config['results_loc'] + "/results/salmon/{sample}", sample=SAMPLES),
		config['results_loc'] + "/results/deseq2/DEseq2_results.RData",
		config['results_loc'] + "/results/deseq2/DEseq2_results_with_names.tsv"

include:	"rules/preprocess.smk"
include:	"rules/salmon.smk"
include:	"rules/deseq2.smk"
include:	"rules/addnames.smk"

onsuccess:
	print("Differential Gene Expression analysis finished!")
	shutil.rmtree(".snakemake")