adding missing modules

9a0ea000 · Brandi Cantarel · 631cfa97 · 9a0ea000
Commit 9a0ea000 authored Sep 29, 2016 by Brandi Cantarel
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workflow/main.nf workflow/main.nf +2 -2

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--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -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
  """
 }