Commit 78048391 authored by peguerin's avatar peguerin
Browse files

debug empty file rule rm_internal_samples

parent 7c07fcb8
...@@ -42,7 +42,7 @@ rule clean_pcrerr_samples: ...@@ -42,7 +42,7 @@ rule clean_pcrerr_samples:
params: params:
r=config["clean_pcrerr_samples"]["r"] r=config["clean_pcrerr_samples"]["r"]
shell: shell:
'''if [[ -s {input} ]]; then obiclean -r {params.r} {input} > {output} 2> {log}; else touch {output} 2> {log}; fi''' '''obiclean -r {params.r} {input} > {output} 2> {log}'''
### Remove sequence which are classified as 'internal' by obiclean ### Remove sequence which are classified as 'internal' by obiclean
rule rm_internal_samples: rule rm_internal_samples:
...@@ -57,5 +57,5 @@ rule rm_internal_samples: ...@@ -57,5 +57,5 @@ rule rm_internal_samples:
log: log:
'../99-log/08-rm_internal_samples/{run}/{sample}.log' '../99-log/08-rm_internal_samples/{run}/{sample}.log'
shell: shell:
''''mkdir -p {params.dir}; if [[ -s {input} ]]; then obigrep -p "obiclean_internalcount == 0" {input} > {output} 2> {log}; fi''' ''''mkdir -p {params.dir}; obigrep -p "obiclean_internalcount == 0" {input} > {output} 2> {log}'''
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