Grab the bam

measles_virus.nf

@@ -142,12 +142,13 @@ process extract_snp {
     output:
     file("*_snp*.tsv") into snpChannel
     file("*_mpileup.vcf.gz") into vcfChannel
+    file("*_nodup.bam"
 
     script:
     """
-    picard MarkDuplicates  -I align_sorted.bam  -O ${read_id}.bam -M marked_dup_metrics.txt --REMOVE_DUPLICATES true 
-    picard BuildBamIndex -I ${read_id}.bam
-    bcftools mpileup --skip-indels -d 10000 -f /local/databases/index/gatk/hg19/2.4-9/hg19.fa ${read_id}.bam -Oz -o  ${read_id}_mpileup.vcf.gz 
+    picard MarkDuplicates  -I align_sorted.bam  -O ${read_id}_nodup.bam -M marked_dup_metrics.txt --REMOVE_DUPLICATES true 
+    picard BuildBamIndex -I ${read_id}_nodup.bam
+    bcftools mpileup --skip-indels -d 10000 -f ${params.human_genome_gatk} ${read_id}_nodup.bam -Oz -o  ${read_id}_mpileup.vcf.gz 
     bcftools call --ploidy 1 -cv -Oz -p 1 -o ${read_id}_calls.vcf.gz ${read_id}_mpileup.vcf.gz 
     bcftools filter -Oz -i 'MIN(DP)>5 && QUAL>10 &&CHROM="chrM"' -o ${read_id}_filt.vcf.gz  ${read_id}_calls.vcf.gz  
     bcftools query -f '%CHROM %POS %REF %ALT %DP4\n' ${read_id}_filt.vcf.gz > ${read_id}_snp_bcf.tsv