Commit 8ba20e15 authored by peguerin's avatar peguerin
Browse files

prevent empty file

parent 2d087661
......@@ -40,7 +40,12 @@ rule clean_pcrerr_samples:
params:
r=config["clean_pcrerr_samples"]["r"]
shell:
'''obiclean -r {params.r} {input} > {output} 2> {log}'''
'''if [ -s {input} ]
then
obiclean -r {params.r} {input} > {output} 2> {log}
else
touch {output} 2> {log}
fi'''
### Remove sequence which are classified as 'internal' by obiclean
rule rm_internal_samples:
......
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