Merge pull request #41 from tcezard/split-prefix

Set large index size for large genomes

variant_to_realignment.nf

@@ -167,6 +167,10 @@ process alignWithMinimap {
         path "reads_aligned.bam", emit: reads_aligned_bam
 
     script:
+    index_size = ""
+    if (file(params.newgenome).size() > 4000000000){
+        index_size = " -I " + file(params.newgenome).size() * 1.1
+    }
     if (flanklength < 500)
         """
         # Options used by the 'sr' preset with some modifications:
@@ -176,15 +180,15 @@ process alignWithMinimap {
         # --secondary=yes -N 2 --> allow up to 2 secondary alignments
         # -y option will take the comment from the fasta entry and output it
         # the awk script will convert this comment in valid SAM tag
-        minimap2 -k21 -w11 --sr --frag=yes -A2 -B5 -O6,16 --end-bonus 20 -E2,1 -r50 -p.5 -z 800,200\
+        minimap2 $index_size -k21 -w11 --sr --frag=yes -A2 -B5 -O6,16 --end-bonus 20 -E2,1 -r50 -p.5 -z 800,200\
                  -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=yes -N 2 -y \
                  -a genome.fa ${reads} | \
                  awk -F '\\t' 'BEGIN{OFS="\\t"}{if(!/^@/){\$NF="vr:Z:"\$NF}; print \$0;}' | \
                  samtools view -bS - > reads_aligned.bam
         """
     else
         """
-        minimap2 -k19 -w19 -A2 -B5 -O6,16 --end-bonus 20 -E3,1 -s200 -z200 -N50 --min-occ-floor=100 \
+        minimap2 $index_size -k19 -w19 -A2 -B5 -O6,16 --end-bonus 20 -E3,1 -s200 -z200 -N50 --min-occ-floor=100 \
                  --secondary=yes -N 2 -y \
                  -a genome.fa ${reads} | \
                  awk -F '\\t' 'BEGIN{OFS="\\t"}{if(!/^@/){\$NF="vr:Z:"\$NF}; print \$0;}' | \