From 81ddca2cc8dea333e410fb368dbc1c8a2a12fbc6 Mon Sep 17 00:00:00 2001
From: rlegendr <rachel.legendre@pasteur.fr>
Date: Fri, 17 Sep 2021 13:09:54 +0200
Subject: [PATCH] gestion of gz
---
Snakefile | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/Snakefile b/Snakefile
index a7ada17..1b22f8d 100755
--- a/Snakefile
+++ b/Snakefile
@@ -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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