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Commit 3b3b88d1 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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fixe issue with input extension

parent 6340bd58
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...@@ -71,9 +71,9 @@ else: ...@@ -71,9 +71,9 @@ else:
sample_dir = config["input_dir"] sample_dir = config["input_dir"]
analysis_dir = config["analysis_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: 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 # global variable for all output files
final_output = [] final_output = []
...@@ -86,9 +86,9 @@ final_output = [] ...@@ -86,9 +86,9 @@ final_output = []
#---------------------------------- #----------------------------------
fastqc_input_fastq = input_data 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_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)) final_output.extend(expand(fastqc_output_done, SAMPLE=samples))
include: os.path.join(RULES, "fastqc.rules") include: os.path.join(RULES, "fastqc.rules")
...@@ -100,9 +100,9 @@ if config["adapters"]["remove"] : ...@@ -100,9 +100,9 @@ if config["adapters"]["remove"] :
adapter_tool = config["adapters"]["tool"] adapter_tool = config["adapters"]["tool"]
adapters_input_fastq = input_data adapters_input_fastq = input_data
adapters_wkdir = "01-Trimming" 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: if paired:
adapters_output += ["01-Trimming/{SAMPLE}_R2_trim.fastq.gz"] adapters_output += ["01-Trimming/{{SAMPLE}}{}_trim{}".format(rt2,config["input_extension"])]
# Set parameters # Set parameters
adapters_options = config["adapters"]["options"] adapters_options = config["adapters"]["options"]
......
...@@ -26,6 +26,15 @@ ...@@ -26,6 +26,15 @@
}, },
"bowtie2_index" : "bowtie2_index" :
{
"ram" : "60G"
},
"kallisto_quant" :
{
"ram" : "30G"
},
"kallisto_index" :
{ {
"ram" : "60G" "ram" : "60G"
} }
......
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