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Commit 88ef1d4d authored by Susheel Busi's avatar Susheel Busi
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edited the ANALYSIS_RULES for running CASC

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2019_GDB/rules/ANALYSIS_RULES
+ 6
− 8
View file @ 88ef1d4d
......@@ -157,7 +157,7 @@ rule casc:
input:
os.path.join(RESULTS_DIR, "assembly/{assembly}.fa")
output:
cas1=os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/{assembly}.results.txt"),
cas1=os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/{assembly}.results.txt")
# cas2=os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/casc_CRISPR_output.txt")
# cas3=directory(os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output"))
log: os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/casc.log")
......@@ -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})
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
"""
rule minced:
......
rules/ANALYSIS_RULES
+ 6
− 8
View file @ 88ef1d4d
......@@ -157,7 +157,7 @@ rule casc:
input:
os.path.join(RESULTS_DIR, "assembly/{assembly}.fa")
output:
cas1=os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/{assembly}.results.txt"),
cas1=os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/{assembly}.results.txt")
# cas2=os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/casc_CRISPR_output.txt")
# cas3=directory(os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output"))
log: os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/casc.log")
......@@ -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})
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
"""
rule minced:
......
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