only provide contaminant and mashmap location if we have something to…

… screen
marbl · Nov 21, 2023 · 7aa9f7f · 7aa9f7f
1 parent f7ddfb1
commit 7aa9f7f
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/src/Snakefiles/7-combineConsensus.sm b/src/Snakefiles/7-combineConsensus.sm
@@ -90,16 +90,19 @@ echo ""
 echo "--------------------"
 echo "Filtering short/disconnected and contaminants."
 echo ""
+screen=""
+if [ "x{params.screens}" != "x" ]; then
+   screen="--contaminant {params.screens} --mashmap {params.MASHMAP}"
+fi
 
 {PERL} {VERKKO}/scripts/screen-assembly.pl \\\\
  --assembly      combined.fasta \\\\
  --graph         ../{input.graph} \\\\
  --graphmap      ../{input.scfmap} \\\\
  --hifi-coverage ../{input.hificov} \\\\
  --minlength     {params.short_len} \\\\
- --contaminant   {params.screens} \\\\
  --output        assembly \\\\
- --mashmap       {params.MASHMAP} \\\\
+ \$screen \\\\
  --threads       {threads} \\\\
 > ./screen-assembly.out 2> ./screen-assembly.err