Commit 64b1dbc4 authored by khalid's avatar khalid
Browse files

remove bug for bowtie SE params

parent 81c86bc7
......@@ -8,7 +8,10 @@ import csv
#############
# Wildcards #
#############
#le nom des sample et les id ne doivent pas contenir de "/" cela evite de boucler dans les arborescences
wildcard_constraints:
sample="[^\/]+",
id="[^\/]+"
STEPS = config["steps"]
PREPARE_REPORT_OUTPUTS = config["prepare_report_outputs"]
PREPARE_REPORT_SCRIPTS = config["prepare_report_scripts"]
......@@ -413,8 +416,8 @@ rule bowtie_SE:
params:
indexPrefix = config["bowtie_index_path"]+"/index",
mult_align_limit = config["bowtie_mult_align_limit"],
best = config["bowtie_best"],
strata = config["bowtie_strata"]
best = "--best" if (config["bowtie_best"]) else "",
strata = "--strata" if (config["bowtie_strata"]) else ""
shell:
"if [ -s {input.read} ]; then "
"bowtie "
......
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