From 3b3b88d106da905aa46c247901c79aa5857d03ba Mon Sep 17 00:00:00 2001
From: rlegendr <rachel.legendre@pasteur.fr>
Date: Thu, 16 Sep 2021 16:08:20 +0200
Subject: [PATCH] fixe issue with input extension
---
Snakefile | 12 ++++++------
config/cluster_config.json | 9 +++++++++
2 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/Snakefile b/Snakefile
index e390896..fca5025 100755
--- a/Snakefile
+++ b/Snakefile
@@ -71,9 +71,9 @@ else:
sample_dir = config["input_dir"]
analysis_dir = config["analysis_dir"]
-input_data = [sample_dir + "/{{SAMPLE}}{}.fastq.gz".format(rt1)]
+input_data = [sample_dir + "/{{SAMPLE}}{}{}".format(rt1,config["input_extension"])]
if paired:
- input_data += [sample_dir + "/{{SAMPLE}}{}.fastq.gz".format(rt2)]
+ input_data += [sample_dir + "/{{SAMPLE}}{}{}".format(rt2,config["input_extension"])]
# global variable for all output files
final_output = []
@@ -86,9 +86,9 @@ final_output = []
#----------------------------------
fastqc_input_fastq = input_data
-fastqc_output_done = "00-Fastqc/{SAMPLE}_R1_fastqc.fastq.gz"
+fastqc_output_done = "00-Fastqc/{{SAMPLE}}{}_fastqc{}".format(rt1,config["input_extension"])
fastqc_wkdir = "00-Fastqc"
-fastqc_log = "00-Fastqc/logs/{SAMPLE}_R1_fastqc_raw.log"
+fastqc_log = "00-Fastqc/logs/{{SAMPLE}}{}_fastqc_raw.log".format(rt1)
final_output.extend(expand(fastqc_output_done, SAMPLE=samples))
include: os.path.join(RULES, "fastqc.rules")
@@ -100,9 +100,9 @@ if config["adapters"]["remove"] :
adapter_tool = config["adapters"]["tool"]
adapters_input_fastq = input_data
adapters_wkdir = "01-Trimming"
- adapters_output = ["01-Trimming/{SAMPLE}_R1_trim.fastq.gz"]
+ adapters_output = ["01-Trimming/{{SAMPLE}}{}_trim{}".format(rt1,config["input_extension"])]
if paired:
- adapters_output += ["01-Trimming/{SAMPLE}_R2_trim.fastq.gz"]
+ adapters_output += ["01-Trimming/{{SAMPLE}}{}_trim{}".format(rt2,config["input_extension"])]
# Set parameters
adapters_options = config["adapters"]["options"]
diff --git a/config/cluster_config.json b/config/cluster_config.json
index 30defdf..94e59c4 100644
--- a/config/cluster_config.json
+++ b/config/cluster_config.json
@@ -26,6 +26,15 @@
},
"bowtie2_index" :
+ {
+ "ram" : "60G"
+ },
+ "kallisto_quant" :
+ {
+ "ram" : "30G"
+ },
+
+ "kallisto_index" :
{
"ram" : "60G"
}
--
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