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xiaowei zhan
rnaseq_variant
Commits
9a0ea000
Commit
9a0ea000
authored
Sep 29, 2016
by
Brandi Cantarel
Browse files
adding missing modules
parent
631cfa97
Changes
1
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workflow/main.nf
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9a0ea000
...
...
@@ -235,12 +235,12 @@ process annotate {
script:
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
"""
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
"""
}
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