two files for paired-end

assembly.smk

@@ -30,18 +30,20 @@ rule khmer:
 def assembly_input(wildcards):
 	if wildcards.reads == "coassembly":
 		if config["NORMALIZATION"]:
-			return [expand("work/khmer/{reads}_R1R2.fastq.gz", reads=config["SAMPLES"])]
+			return {"R1R2": expand("work/khmer/{reads}_R1R2.fastq.gz", reads=config["SAMPLES"])}
 		elif config["SORTMERNA"]:
-			return [expand("work/sortmerna/{reads}_mRNA.fastq.gz", reads=config["SAMPLES"])]
+			return {"R1R2": expand("work/sortmerna/{reads}_mRNA.fastq.gz", reads=config["SAMPLES"])}
 		else:
-			return [expand("DATA/trim/{reads}_R1R2.fastq.gz", reads=config["SAMPLES"])]
+			return {"R1": expand("DATA/trim/{reads}_R1.fastq.gz", reads=config["SAMPLES"]), "R2": expand("DATA/trim/{reads}_R2.fastq.gz", reads=config["SAMPLES"])}
+
 	else:
 		if config["NORMALIZATION"]:
-			return {"R1R2": "work/khmer/{wildcards.reads}_R1R2.fastq.gz".format(wildcards=wildcards)}
+			return {"R1R2": ["work/khmer/{wildcards.reads}_R1R2.fastq.gz".format(wildcards=wildcards)]}
 		elif config["SORTMERNA"]:
-			return {"R1R2": "work/sortmerna/{wildcards.reads}_mRNA.fastq.gz".format(wildcards=wildcards)}
+			return {"R1R2": ["work/sortmerna/{wildcards.reads}_mRNA.fastq.gz".format(wildcards=wildcards)]}
 		else:
-			return {"R1R2": "DATA/trim/{wildcards.reads}_R1R2.fastq.gz".format(wildcards=wildcards)}
+			return {"R1": ["DATA/trim/{wildcards.reads}_R1.fastq.gz".format(wildcards=wildcards)], "R2": ["DATA/trim/{wildcards.reads}_R2.fastq.gz".format(wildcards=wildcards)]}
+
 
 rule megahit:
 	input:
@@ -53,11 +55,11 @@ rule megahit:
 	params:
 		min_len = config["CONTIGS_LEN"],
 		mem_tot = int(250 * 1e9),
-		input = lambda wildcards, input: ",".join(input),
+		input = lambda wildcards, input: "-1 %s -2 %s"%(",".join(input.R1), ",".join(input.R2)) if set(['R1', 'R2']).issubset(input.keys()) else "--12 %s"%",".join(input.R1R2),
 		output = lambda wildcards, output: os.path.dirname(str(output.contigs))
 	shell:
 		"megahit "
-		"--12 {params.input} "
+		"{params.input} "
 		"--continue "
 		"--preset meta-large "
 		"--num-cpu-threads {threads} "
@@ -78,7 +80,7 @@ rule metaspades:
 	params:
 		min_len = config["CONTIGS_LEN"],
 		mem_tot = 250,
-		input = lambda wildcards, input: " --12 ".join(input),
+		input = lambda wildcards, input: "-1 %s -2 %s"%(" -1 ".join(input.R1), " -2 ".join(input.R2)) if set(['R1', 'R2']).issubset(input.keys()) else "--12 %s"%" --12 ".join(input.R1R2),
 		output = lambda wildcards, output: os.path.dirname(str(output.contigs))
 	shell:
 		"spades.py "
@@ -86,7 +88,7 @@ rule metaspades:
 		"--memory {params.mem_tot} "
 		"--tmp-dir /projet/tmp "
 		"--meta "
-		"--12 {params.input} "
+		"{params.input} "
 		"-o {params.output} "
 		" ; "
 		"filterSeq.py "