Mercurial > repos > estrain > microrunqc

diff microrunqc.xml @ 21:5083f8406e34 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Fri, 19 Jan 2024 11:47:29 +0000
parents b07d5fec5942
children
line wrap: on
line diff
--- a/microrunqc.xml	Thu Jan 18 20:20:40 2024 +0000
+++ b/microrunqc.xml	Fri Jan 19 11:47:29 2024 +0000
@@ -105,7 +105,7 @@
     #end if
     ${outname}.fasta > ${outname}.mlst_raw.tsv;
     
-    perl $__tool_directory__/mlstAddFields.pl ${outname}.mlst_raw.tsv > ${outname}.mlst.tsv;
+    python $__tool_directory__/mlstAddFields.py ${outname}.mlst_raw.tsv $mlst_databases.fields.path/pubmlst > ${outname}.mlst.tsv;
 
     python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan};