fix bug in miniasm rule

pmenzel · Jan 25, 2024 · 8b731e3 · 8b731e3
1 parent bac81b2
commit 8b731e3
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diff --git a/README.md b/README.md
@@ -183,7 +183,8 @@ Unicycler does a hybrid assembly, i.e., both ONT and Illumina reads must be pres
 ### Canu
 
 **`canu`**  
-The Canu assembler requires to know the genome size (in Megabases) beforehand, use Snakemake option: `--config genome_size=5.2` (e.g. for 5.2 Mb)
+The Canu assembler requires to know the genome size (in Megabases) beforehand, use Snakemake option: `--config genome_size=5.2` (e.g. for 5.2 Mb)  
+NB: Canu can take a long time to complete the assembly, up to several hours!
 
 ### racon
 Following keywords can be used to polish an assembly using ONT reads:

diff --git a/Snakefile b/Snakefile
@@ -290,7 +290,7 @@ rule miniasm:
     shell:
         """
         minimap2 -x ava-ont -t {threads} {input} {input} > {output.paf} 2>{log}
-        miniasm -f {input} {output.paf} > {output..gfa} 2>>{log}
+        miniasm -f {input} {output.paf} > {output.gfa} 2>>{log}
         perl -lsane 'print ">$F[1]\n$F[2]" if $F[0] =~ /S/;' {output.gfa} > {output.fa} 2>>{log}
         ln -sr {output.fa} {output.link}
         """