Commit 761ad1a1 authored by peguerin's avatar peguerin
Browse files

ultime tentative jpp

parent 44ef8782
......@@ -42,7 +42,7 @@ 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:
......@@ -57,5 +57,5 @@ rule rm_internal_samples:
log:
'../99-log/08-rm_internal_samples/{run}/{sample}.log'
shell:
'''mkdir -p {params.dir}; obigrep -p "obiclean_internalcount == 0" {input} > {output} 2> {log}'''
'''if [[ -s {input} ]]; then mkdir -p {params.dir}; obigrep -p "obiclean_internalcount == 0" {input} > {output} 2> {log}'''
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