Fix typo in UnifiedGenotyper IndelRealigner command

Changed {samplenane} to {samplename} (line 2337)

Author: IdoBar

main.nf

@@ -2334,7 +2334,7 @@ process genotyping_ug {
     """
     samtools index ${bam}
     gatk3 -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
-    gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplenane}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
+    gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplename}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
     gatk3 -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --dbsnp ${params.gatk_dbsnp} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
     
     $keep_realign