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Commit 81ddca2c authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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gestion of gz

parent 27660897
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......@@ -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}}{}_trim{}".format(rt1,config["input_extension"])]
adapters_output = ["01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt1)]
if paired:
adapters_output += ["01-Trimming/{{SAMPLE}}{}_trim{}".format(rt2,config["input_extension"])]
adapters_output += ["01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt2)]
# Set parameters
adapters_options = config["adapters"]["options"]
......@@ -131,8 +131,8 @@ else:
if config["genome"]["rRNA_mapping"] :
sortmerna_input = adapters_output
sortmerna_fasta = config["genome"]["ribo_fasta_file"]
sortmerna_outfile_rRNA = "02-Mapping/Ribo/{SAMPLE}_rRNA.fastq.gz"
sortmerna_outfile_no_rRNA = "02-Mapping/Ribo/{SAMPLE}_norRNA.fastq.gz"
sortmerna_outfile_rRNA = "02-Mapping/Ribo/{SAMPLE}_rRNA.fastq"
sortmerna_outfile_no_rRNA = "02-Mapping/Ribo/{SAMPLE}_norRNA.fastq"
sortmerna_logs_err = "02-Mapping/Ribo/logs/{SAMPLE}_mapping.err"
sortmerna_logs_out = "02-Mapping/Ribo/logs/{SAMPLE}_mapping.out"
final_output.extend(expand(sortmerna_outfile_no_rRNA, SAMPLE=samples))
......
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