Fixed consensus generation for VarScan2 and Bcftools masking referenc…

…e genome in the first place.

main.nf

@@ -1385,17 +1385,18 @@ process VARSCAN2_CONSENSUS {
     script:
     prefix = "${sample}.AF${params.max_allele_freq}"
     """
-    cat $fasta | bcftools consensus ${vcf[0]} > ${prefix}.consensus.fa
-
     bedtools genomecov \\
         -bga \\
         -ibam ${bam[0]} \\
+        -g $fasta \\
         | awk '\$4 < $params.min_coverage' | bedtools merge > ${prefix}.mask.bed
 
     bedtools maskfasta \\
-        -fi ${prefix}.consensus.fa \\
+        -fi $fasta \\
         -bed ${prefix}.mask.bed \\
-        -fo ${prefix}.consensus.masked.fa
+        -fo ${index_base}.ref.masked.fa
+    cat ${index_base}.ref.masked.fa | bcftools consensus ${vcf[0]} > ${prefix}.consensus.masked.fa
+
     header=\$(head -n 1 ${prefix}.consensus.masked.fa | sed 's/>//g')
     sed -i "s/\${header}/${sample}/g" ${prefix}.consensus.masked.fa
 
@@ -1782,17 +1783,18 @@ process BCFTOOLS_CONSENSUS {
 
     script:
     """
-    cat $fasta | bcftools consensus ${vcf[0]} > ${sample}.consensus.fa
-
     bedtools genomecov \\
         -bga \\
         -ibam ${bam[0]} \\
+        -g $fasta \\
         | awk '\$4 < $params.min_coverage' | bedtools merge > ${sample}.mask.bed
 
     bedtools maskfasta \\
-        -fi ${sample}.consensus.fa \\
+        -fi $fasta \\
         -bed ${sample}.mask.bed \\
-        -fo ${sample}.consensus.masked.fa
+        -fo ${index_base}.ref.masked.fa
+    cat ${index_base}.ref.masked.fa | bcftools consensus ${vcf[0]} > ${sample}.consensus.masked.fa
+
     sed -i 's/${index_base}/${sample}/g' ${sample}.consensus.masked.fa
     header=\$(head -n1 ${sample}.consensus.masked.fa | sed 's/>//g')
     sed -i "s/\${header}/${sample}/g" ${sample}.consensus.masked.fa