Snakefile

#!/usr/bin/env python

import os
import sys
import re
import glob

configfile: "config.yaml"

### 

extension = config["extension"]

FILES = [ os.path.basename(x) for x in glob.glob("Experience/*") ] 

if config["design"]["paired"]:
	SAMPLES = list(set([ "_".join(x.split("_")[:2]) for x in FILES]))
else:
	SAMPLES = list(set([ x.rstrip(extension) for x in FILES]))

DIR_COMPARAISON = "DAS/"+config["design"]["condition_1"]+"_VS_"+config["design"]["condition_2"]

###

def get_input(wildcards):
	input_list = ["Reference/reference.fasta"]

	for fq in expand("Trimming/{sample}_R1.trim.fastq.gz", sample=SAMPLES):
		input_list.append(fq)

	if config["DEG"]["exec"]:
		input_list.append("DEG/tair_ids.txt")
		
	if config["DTU"]["exec"]:
		input_list.append("DTU/DTU.txt")

	if config["DASG"]["exec"]:
		for fq_AS in expand("Trimming_AS/{sample}_R1.trim.fastq.gz", sample=SAMPLES):
			input_list.append(fq_AS)
		input_list.append("DAS/DAS.txt")

	if config["CSE"]["exec"]:
		input_list.append("CSE_results/CSE_DEG_UP.txt")

	return input_list


include: "rules/get_packages.smk"
include: "rules/get_ref_files.smk"

if config["trimming"]["exec"]:
	include: "rules/trimming.smk"

if config["DEG"]["exec"]:
	include: "rules/classic_mapping.smk"
	include: "rules/counts.smk"
	include: "rules/run_DESeq2.smk"



if config["DASG"]["exec"]:
	include: "rules/trimming_AS.smk"
	include: "rules/1st_pass.smk"
	include: "rules/2sd_pass.smk"
	include: "rules/run_rMATS.smk"
	include: "rules/sign_DAS.smk"

if config["DTU"]["exec"]:
	include: "rules/salmon_pseudomapping.smk"
	include: "rules/run_RATs.smk"

if config["CSE"]["exec"]:
	include: "rules/init_CSE.smk"
	

rule all:	
	input:
		get_input