From d176e65db6a4cb39824dfa1b4ea946792572d1bd Mon Sep 17 00:00:00 2001
From: rlegendr <rachel.legendre@pasteur.fr>
Date: Fri, 17 Sep 2021 13:18:05 +0200
Subject: [PATCH] fixe path in star index
---
Snakefile | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/Snakefile b/Snakefile
index 1b22f8d..f57d18c 100755
--- a/Snakefile
+++ b/Snakefile
@@ -86,7 +86,7 @@ final_output = []
#----------------------------------
fastqc_input_fastq = input_data
-fastqc_output_done = "00-Fastqc/{{SAMPLE}}{}_fastqc{}".format(rt1,config["input_extension"])
+fastqc_output_done = "00-Fastqc/{{SAMPLE}}{}_fastqc.done".format(rt1)
fastqc_wkdir = "00-Fastqc"
fastqc_log = "00-Fastqc/logs/{{SAMPLE}}{}_fastqc_raw.log".format(rt1)
final_output.extend(expand(fastqc_output_done, SAMPLE=samples))
@@ -212,8 +212,8 @@ if config["star_mapping"]["do"]:
star_index_fasta = unpack(mapping_index)
star_mapping_splice_file = unpack(annot_index)
star_index_log = "02-Mapping/{REF}/STAR/logs/STAR_{REF}_indexing.log"
- star_index_output_done = config["genome"]["genome_directory"]+"/{REF}/STAR/SAindex"
- star_index_output_dir = config["genome"]["genome_directory"]+"/{REF}/STAR/"
+ star_index_output_done = os.path.join(config["genome"]["genome_directory"], "/{REF}/STAR/SAindex")
+ star_index_output_dir = os.path.join(config["genome"]["genome_directory"], "/{REF}/STAR/")
include: os.path.join(RULES, "star_index.rules")
--
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