diff --git a/rules/ANALYSIS_RULES b/rules/ANALYSIS_RULES index 33d507226b32c22c5376034dd0c3ecfd98ee671e..f68b057d61660cc8d1cddddd39cf6fdf056b49e4 100755 --- a/rules/ANALYSIS_RULES +++ b/rules/ANALYSIS_RULES @@ -168,8 +168,8 @@ rule casc: export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin &&\ export PERL5LIB=/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative &&\ - echo $(basename -s "" {output}) >> {output.cas2} &&\ - awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output} >> {output.cas2} &&\ + echo $(basename -s "" {output.cas1}) >> {output.cas2} &&\ + awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\ date) &> >(tee {log}) """