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Commit aeb752cd authored by Susheel Busi's avatar Susheel Busi
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removing the date flag from CASC shell due to errors

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2019_GDB/rules/ANALYSIS_RULES
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View file @ aeb752cd
...@@ -165,13 +165,11 @@ rule casc: ...@@ -165,13 +165,11 @@ rule casc:
conda: "../envs/analysis.yaml" conda: "../envs/analysis.yaml"
shell: shell:
""" """
(date
export PATH={config[CASC][PATH]} export PATH={config[CASC][PATH]}
export PERL5LIB={config[CASC][PERL5LIB]} export PERL5LIB={config[CASC][PERL5LIB]}
casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative 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 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 cat {output.cas1} | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> results/analysis/crispr/casc/casc_CRISPR_output.txt
date) &> >(tee {log})
""" """
rule minced: rule minced:
......
rules/ANALYSIS_RULES
+ 0
− 2
View file @ aeb752cd
...@@ -165,13 +165,11 @@ rule casc: ...@@ -165,13 +165,11 @@ rule casc:
conda: "../envs/analysis.yaml" conda: "../envs/analysis.yaml"
shell: shell:
""" """
(date
export PATH={config[CASC][PATH]} export PATH={config[CASC][PATH]}
export PERL5LIB={config[CASC][PERL5LIB]} export PERL5LIB={config[CASC][PERL5LIB]}
casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative 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 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 cat {output.cas1} | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> results/analysis/crispr/casc/casc_CRISPR_output.txt
date) &> >(tee {log})
""" """
rule minced: rule minced:
......
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