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Commit a44ac1ab authored by BIOPZ-Gypas Foivos's avatar BIOPZ-Gypas Foivos
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Small changes

parent 81ba7bd8
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...@@ -39,7 +39,7 @@ rule clip_reads: ...@@ -39,7 +39,7 @@ rule clip_reads:
flag = config["dir_created"], flag = config["dir_created"],
reads = os.path.join(config["input_dir"], "{sample}" + config["input_reads_pattern"]), reads = os.path.join(config["input_dir"], "{sample}" + config["input_reads_pattern"]),
output: 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: params:
v = "-v", v = "-v",
n = "-n", n = "-n",
...@@ -59,7 +59,6 @@ rule clip_reads: ...@@ -59,7 +59,6 @@ rule clip_reads:
-l {params.l} \ -l {params.l} \
{params.qual} \ {params.qual} \
-a {params.adapter} \ -a {params.adapter} \
{params.z} \
-i <(zcat {input.reads}) \ -i <(zcat {input.reads}) \
-o {output.reads}) &> {log}" -o {output.reads}) &> {log}"
...@@ -69,9 +68,9 @@ rule clip_reads: ...@@ -69,9 +68,9 @@ rule clip_reads:
rule trim_reads: rule trim_reads:
input: 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: 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: params:
v = "-v", v = "-v",
l = "20", l = "20",
...@@ -89,8 +88,7 @@ rule trim_reads: ...@@ -89,8 +88,7 @@ rule trim_reads:
-l {params.l} \ -l {params.l} \
-t {params.t} \ -t {params.t} \
{params.qual} \ {params.qual} \
{params.z} \ -i {input.reads} \
-i <(zcat {input.reads}) \
-o {output.reads}) &> {log}" -o {output.reads}) &> {log}"
################################################################################# #################################################################################
...@@ -99,15 +97,14 @@ rule trim_reads: ...@@ -99,15 +97,14 @@ rule trim_reads:
rule filter_reads: rule filter_reads:
input: 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: 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: params:
v = "-v", v = "-v",
q = "20", q = "20",
p = "90", p = "90",
qual = "-Q33", qual = "-Q33",
z = "-z",
cluster_log = os.path.join(config["cluster_log"], "filter_reads_{sample}.log") cluster_log = os.path.join(config["cluster_log"], "filter_reads_{sample}.log")
log: log:
os.path.join(config["local_log"], "filter_reads_{sample}.log") os.path.join(config["local_log"], "filter_reads_{sample}.log")
...@@ -119,8 +116,7 @@ rule filter_reads: ...@@ -119,8 +116,7 @@ rule filter_reads:
-q {params.q} \ -q {params.q} \
-p {params.p} \ -p {params.p} \
{params.qual} \ {params.qual} \
{params.z} \ -i {input.reads} \
-i <(zcat {input.reads}) \
-o {output.reads}) &> {log}" -o {output.reads}) &> {log}"
################################################################################# #################################################################################
...@@ -129,7 +125,7 @@ rule filter_reads: ...@@ -129,7 +125,7 @@ rule filter_reads:
rule fastq_to_fasta: rule fastq_to_fasta:
input: 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: output:
reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fasta"), reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fasta"),
params: params:
...@@ -149,7 +145,7 @@ rule fastq_to_fasta: ...@@ -149,7 +145,7 @@ rule fastq_to_fasta:
{params.qual} \ {params.qual} \
{params.n} \ {params.n} \
{params.r} \ {params.r} \
-i <(zcat {input.reads}) \ -i {input.reads} \
-o {output.reads}) &> {log}" -o {output.reads}) &> {log}"
################################################################################# #################################################################################
...@@ -190,7 +186,7 @@ rule map_to_other_genes: ...@@ -190,7 +186,7 @@ rule map_to_other_genes:
rule map_to_transcripts: rule map_to_transcripts:
input: 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"], index = config["transcripts_index"],
sequence = config["transcripts_sequence"] sequence = config["transcripts_sequence"]
output: output:
......
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
"queue":"6hours", "queue":"6hours",
"time": "05:00:00", "time": "05:00:00",
"threads":"1", "threads":"1",
"mem":"4G" "mem":"8G"
}, },
"map_to_other_genes": "map_to_other_genes":
{ {
......
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