Commit 9a0ea000 authored by Brandi Cantarel's avatar Brandi Cantarel

adding missing modules

parent 631cfa97
...@@ -235,12 +235,12 @@ process annotate { ...@@ -235,12 +235,12 @@ process annotate {
script: script:
if (params.genome == '/project/shared/bicf_workflow_ref/GRCh38') if (params.genome == '/project/shared/bicf_workflow_ref/GRCh38')
""" """
module load snpeff/4.2 module load python/2.7.x-anaconda snpeff/4.2
java -Xmx10g -jar \$SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c \$SNPEFF_HOME/snpEff.config ${snpeff_vers} final.integrate.vcf.gz | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar annotate ${index_path}/dbSnp.vcf.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar annotate ${index_path}/clinvar.vcf.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar annotate ${index_path}/ExAC.vcf.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar annotate ${index_path}/cosmic.vcf.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar gwasCat -db ${index_path}/gwas_catalog.tsv - |bgzip > annot.vcf.gz java -Xmx10g -jar \$SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c \$SNPEFF_HOME/snpEff.config ${snpeff_vers} final.integrate.vcf.gz | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar annotate ${index_path}/dbSnp.vcf.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar annotate ${index_path}/clinvar.vcf.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar annotate ${index_path}/ExAC.vcf.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar annotate ${index_path}/cosmic.vcf.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar gwasCat -db ${index_path}/gwas_catalog.tsv - |bgzip > annot.vcf.gz
""" """
else else
""" """
module load snpeff/4.2 module load python/2.7.x-anaconda snpeff/4.2
java -Xmx10g -jar \$SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c \$SNPEFF_HOME/snpEff.config ${snpeff_vers} final.integrate.vcf.gz |bgzip > annot.vcf.gz java -Xmx10g -jar \$SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c \$SNPEFF_HOME/snpEff.config ${snpeff_vers} final.integrate.vcf.gz |bgzip > annot.vcf.gz
""" """
} }
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