--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mashmap.bash.txt	Sat Feb 24 08:20:07 2024 +0000
@@ -0,0 +1,21 @@
+ln -s '$query' 'query' &&
+#if len($reflist) > 1:
+#for i, mash in enumerate($reflist):
+   #if i == 0:
+       echo '$mash' > 'reflist' &&
+   #else:
+       echo '$mash' >> 'reflist' &&
+   #end if
+#end for
+#end if
+samtools faidx 'query' &&
+mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
+#if int($sketchSize) > 0:
+-J '$sketchSize' \
+#end if
+#if len($reflist) == 1:
+ -r '$reflist' -q 'query' && 
+#else
+--rl 'reflist' -q 'query' && 
+#end if
+cp 'mashmap.out'  '$mashout'