Small changes

snakemake/process_data/Snakefile

@@ -39,7 +39,7 @@ rule clip_reads:
 		flag = config["dir_created"],
 		reads = os.path.join(config["input_dir"], "{sample}" + config["input_reads_pattern"]),
 	output:
-		reads = os.path.join(config["output_dir"], "{sample}/pro.clipped.fastq.gz"),
+		reads = os.path.join(config["output_dir"], "{sample}/pro.clipped.fastq"),
 	params:
 		v = "-v",
 		n = "-n",
@@ -59,7 +59,6 @@ rule clip_reads:
 		-l {params.l} \
 		{params.qual} \
 		-a {params.adapter} \
-		{params.z} \
 		-i <(zcat {input.reads}) \
 		-o {output.reads}) &> {log}"
 
@@ -69,9 +68,9 @@ rule clip_reads:
 
 rule trim_reads:
 	input:
-		reads = os.path.join(config["output_dir"], "{sample}/pro.clipped.fastq.gz")
+		reads = os.path.join(config["output_dir"], "{sample}/pro.clipped.fastq")
 	output:
-		reads = os.path.join(config["output_dir"], "{sample}/pro.trimmed.fastq.gz"),
+		reads = os.path.join(config["output_dir"], "{sample}/pro.trimmed.fastq"),
 	params:
 		v = "-v",
 		l = "20",
@@ -89,8 +88,7 @@ rule trim_reads:
 		-l {params.l} \
 		-t {params.t} \
 		{params.qual} \
-		{params.z} \
-		-i <(zcat {input.reads}) \
+		-i {input.reads} \
 		-o {output.reads}) &> {log}"
 
 #################################################################################
@@ -99,15 +97,14 @@ rule trim_reads:
 
 rule filter_reads:
 	input:
-		reads = os.path.join(config["output_dir"], "{sample}/pro.trimmed.fastq.gz"),
+		reads = os.path.join(config["output_dir"], "{sample}/pro.trimmed.fastq"),
 	output:
-		reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fastq.gz"),
+		reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fastq"),
 	params:
 		v = "-v",
 		q = "20",
 		p = "90",
 		qual = "-Q33",
-		z = "-z",
 		cluster_log = os.path.join(config["cluster_log"], "filter_reads_{sample}.log")
 	log:
 		os.path.join(config["local_log"], "filter_reads_{sample}.log")
@@ -119,8 +116,7 @@ rule filter_reads:
 		-q {params.q} \
 		-p {params.p} \
 		{params.qual} \
-		{params.z} \
-		-i <(zcat {input.reads}) \
+		-i {input.reads} \
 		-o {output.reads}) &> {log}"
 
 #################################################################################
@@ -129,7 +125,7 @@ rule filter_reads:
 
 rule fastq_to_fasta:
 	input:
-		reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fastq.gz"),
+		reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fastq"),
 	output:
 		reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fasta"),
 	params:
@@ -149,7 +145,7 @@ rule fastq_to_fasta:
 		{params.qual} \
 		{params.n} \
 		{params.r} \
-		-i <(zcat {input.reads}) \
+		-i {input.reads} \
 		-o {output.reads}) &> {log}"
 
 #################################################################################
@@ -190,7 +186,7 @@ rule map_to_other_genes:
 
 rule map_to_transcripts:
 	input:
-		reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fasta"),
+		reads = os.path.join(config["output_dir"], "{sample}/other_genes.unmapped.fasta"),
 		index = config["transcripts_index"],
 		sequence = config["transcripts_sequence"]
 	output:

snakemake/process_data/cluster.json

@@ -4,7 +4,7 @@
 "queue":"6hours",
 "time": "05:00:00",
 "threads":"1",
-"mem":"4G"
+"mem":"8G"
 },
 "map_to_other_genes":
 {