adding missing modules

workflow/main.nf

@@ -152,7 +152,7 @@ process gatk {
   file("final.gatkpanel.vcf.gz") into gatkvcf
   script:
   """
-  module load gatk/3.5 bedtools/2.25.0 snpeff/4.2 vcftools/0.1.11 
+  module load gatk/3.5 bedtools/2.25.0 python/2.7.x-anaconda snpeff/4.2 vcftools/0.1.11 
   java -Xmx16g -jar \$GATK_JAR -R ${gatkref} -D ${dbsnp} -T GenotypeGVCFs -o final.gatk.vcf -nt 4 --variant ${(gvcf as List).join(' --variant ')}
   java -Xmx16g -jar \$GATK_JAR -R ${gatkref} -T VariantFiltration -V final.gatk.vcf -window 35 -cluster 3 -filterName FS -filter "FS > 30.0" -filterName QD -filter "QD < 2.0" -o final.filtgatk.vcf 
   vcf-annotate -n --fill-type final.filtgatk.vcf | java -jar \$SNPEFF_HOME/SnpSift.jar filter '((QUAL >= 10) & (MQ > 40) & (DP >= 10))' |bgzip > final.gatkpanel.vcf.gz
@@ -171,7 +171,7 @@ process mpileup {
   file("final.sampanel.vcf.gz") into samvcf
   script:
   """
-  module load samtools/intel/1.3 bedtools/2.25.0 bcftools/intel/1.3 snpeff/4.2 vcftools/0.1.11
+  module load python/2.7.x-anaconda samtools/intel/1.3 bedtools/2.25.0 bcftools/intel/1.3 snpeff/4.2 vcftools/0.1.11
   ls *.bam > final.bam.list
   samtools mpileup -t 'AD,ADF,ADR,INFO/AD,SP' -ug -Q20 -C50 -f ${index_path}/genome.fa -b final.bam.list | bcftools call --format-fields gq,gp -vmO z -o final.sam.vcf.gz
   vcf-annotate -n --fill-type final.sam.vcf.gz | java -jar \$SNPEFF_HOME/SnpSift.jar filter '((QUAL >= 10) & (MQ >= 20) & (DP >= 10))' |bgzip > final.sampanel.vcf.gz
@@ -190,7 +190,7 @@ process speedseq {
   file("final.complex.vcf.gz") into complexvcf
   script:
   """
-  module load samtools/intel/1.3 bedtools/2.25.0 bcftools/intel/1.3 snpeff/4.2 speedseq/20160506 vcftools/0.1.11
+  module load python/2.7.x-anaconda samtools/intel/1.3 bedtools/2.25.0 bcftools/intel/1.3 snpeff/4.2 speedseq/20160506 vcftools/0.1.11
   speedseq var -q 10 -t 32 -o final.ssvar ${index_path}/genome.fa ${gbam}
   vcf-annotate -n --fill-type -n final.ssvar.vcf.gz | java -jar \$SNPEFF_HOME/SnpSift.jar filter '((QUAL >= 10) & (DP >= 10))' |bgzip > final.sspanel.vcf.gz
   java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar filter "(TYPE='complex')" final.sspanel.vcf.gz |bgzip> final.complex.vcf.gz
@@ -210,7 +210,7 @@ process integrate {
   file("final.integrate.vcf.gz") into finalvcf
   script:
   """
-  module load bedtools/2.25.0 snpeff/4.2 bcftools/intel/1.3 samtools/intel/1.3 jags/4.2.0
+  module load python/2.7.x-anaconda bedtools/2.25.0 snpeff/4.2 bcftools/intel/1.3 samtools/intel/1.3 jags/4.2.0
   module load vcftools/0.1.11
   zcat ${ssvcf} | bedtools intersect -v -header -a stdin -b ${complex} | bgzip > ss.shuff.vcf.gz
   vcf-shuffle-cols -t ${ssvcf} ${gvcf} | vcf-sort | bedtools intersect -v -header -a stdin -b ${complex} | bgzip > gatk.shuff.vcf.gz