adding gatk module load

workflow/main.nf

@@ -136,6 +136,7 @@ process gatkgvcf {
   file("${pair_id}.gatk.g.vcf") into gatkgvcf
   script:
   """
+  module load gatk/3.5
   java -Xmx10g -jar \$GATK_JAR -R ${gatkref} -D ${dbsnp} -T HaplotypeCaller -stand_call_conf 20 -stand_emit_conf 20.0 -dontUseSoftClippedBases -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -variant_index_type LINEAR -variant_index_parameter 128000 --emitRefConfidence GVCF -I ${gbam} -o ${pair_id}.gatk.g.vcf -L ${genebed}
   """
 }
@@ -234,12 +235,12 @@ process annotate {
   script:
   if (params.genome == '/project/shared/bicf_workflow_ref/GRCh38')
   """
-  module load bedtools/2.25.0 snpeff/4.2 jags/4.2.0
+  module load 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
   """
-  java -Xmx10g -jar \$SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c \$SNPEFF_HOME/snpEff.config ${snpeff_vers} final.integrate.vcf.gz |bgz
-ip > annot.vcf.gz
+  module load 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
   """
 }