change fasta header also for Sanger and consensus

aknijn · Apr 1, 2021 · df77f5e · df77f5e
1 parent 3fcaffb
commit df77f5e
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diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,5 @@ RECoVGISAID/gisaid_uploader.py
 RECoVGISAID/recovgisaid-pre.xml
 RECoVGISAID/RECoVGISAID.py
 RECoVGISAID/recovgisaid.xml
+RECoVGISAID/recovgisaid_hospitals
+RECoVGISAID/recovgisaid_users
diff --git a/tools/ivar_covid_consensus.xml b/tools/ivar_covid_consensus.xml
@@ -17,8 +17,8 @@
 		#else:
             ln -s '$input_bam' sorted.bam &&
             samtools mpileup -A -d 0 -Q 0 sorted.bam | ivar consensus -p consensus -t 0.2 -n N -q 20 -m 30 &&
-            sed -i "1s|.*|>$clean_name|" consensus.fa
         #end if    
+        sed -i "1s|.*|>$clean_name|" consensus.fa
     ]]>    </command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>