Mercurial > repos > greg > cfsan_snp_pipeline_call_consensus_snps

comparison cfsan_snp_pipeline_call_consensus_snps.xml @ 2:d2ac1f5c05ed draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 23 Nov 2023 22:11:08 +0000
parents 0fd0a757072c
children
comparison
equal deleted inserted replaced
1:0fd0a757072c 2:d2ac1f5c05ed
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #set $identifier = $input_call_pileup.element_identifier 8 #set identifier = $input_call_pileup.element_identifier
9 mkdir -p ./$identifier/ && 9 mkdir -p ./'$identifier'/ &&
10 cp '$input_call_pileup' ./'$identifier'/reads.all.pileup && 10 cp '$input_call_pileup' ./'$identifier'/reads.all.pileup &&
11 cfsan_snp_pipeline call_consensus -v 4 -l '$input_merged_snp_sites' --vcfFileName 'consensus.vcf' ./'$identifier'/reads.all.pileup 1>&2 && 11 cfsan_snp_pipeline call_consensus -v 4 -l '$input_merged_snp_sites' --vcfFileName 'consensus.vcf' ./'$identifier'/reads.all.pileup 1>&2 &&
12 mv ./consensus.fasta '$output_fasta' && 12 mv ./consensus.fasta '$output_fasta' &&
13 mv ./consensus.vcf '$output_vcf' 13 mv ./consensus.vcf '$output_vcf'
14 ]]></command> 14 ]]></command>