Mercurial > repos > iuc > artic_minion

diff artic_minion.xml @ 7:f5643712dca7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
author iuc
date Mon, 31 Jan 2022 10:12:30 +0000
parents f212134e204c
children 6f52ebc01098
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--- a/artic_minion.xml	Wed Oct 06 12:04:58 2021 +0000
+++ b/artic_minion.xml	Mon Jan 31 10:12:30 2022 +0000
@@ -34,8 +34,13 @@
             --medaka-model '$medaka_model'
             $bwa
             'name/V1'
-            '${read_file.element_identifier}'
+            ## enclose the sample name in extra single quotes because
+            ## the minion pipeline script doesn't care about passing
+            ## its arguments safely.
+            "'"'${read_file.element_identifier}'"'"
         && bgzip -f '${read_file.element_identifier}.fail.vcf'
+        ## remove enclosing single-quotes from header of output consensus fasta
+        && sed -i "1s/'${read_file.element_identifier}'/${read_file.element_identifier}/" ${read_file.element_identifier}.consensus.fasta
     ]]></command>
     <inputs>
         <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>