diff --git a/2019_GDB/rules/ANALYSIS_RULES b/2019_GDB/rules/ANALYSIS_RULES index d1eb5734fc72462b88be17c55045b39f0d95af12..d5fda4700ede8a6162d0c193c90c643ca50f9abb 100755 --- a/2019_GDB/rules/ANALYSIS_RULES +++ b/2019_GDB/rules/ANALYSIS_RULES @@ -165,13 +165,11 @@ rule casc: conda: "../envs/analysis.yaml" shell: """ - (date export PATH={config[CASC][PATH]} export PERL5LIB={config[CASC][PERL5LIB]} casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative echo $(basename -s ".results.txt" {output.cas1}) >> results/analysis/crispr/casc/casc_CRISPR_output.txt cat {output.cas1} | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> results/analysis/crispr/casc/casc_CRISPR_output.txt - date) &> >(tee {log}) """ rule minced: diff --git a/rules/ANALYSIS_RULES b/rules/ANALYSIS_RULES index d1eb5734fc72462b88be17c55045b39f0d95af12..d5fda4700ede8a6162d0c193c90c643ca50f9abb 100755 --- a/rules/ANALYSIS_RULES +++ b/rules/ANALYSIS_RULES @@ -165,13 +165,11 @@ rule casc: conda: "../envs/analysis.yaml" shell: """ - (date export PATH={config[CASC][PATH]} export PERL5LIB={config[CASC][PERL5LIB]} casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative echo $(basename -s ".results.txt" {output.cas1}) >> results/analysis/crispr/casc/casc_CRISPR_output.txt cat {output.cas1} | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> results/analysis/crispr/casc/casc_CRISPR_output.txt - date) &> >(tee {log}) """ rule minced: