Mercurial > repos > greg > cfsan_snp_pipeline_call_consensus_snps
comparison cfsan_snp_pipeline_call_consensus_snps.xml @ 2:d2ac1f5c05ed draft default tip
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author | greg |
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date | Thu, 23 Nov 2023 22:11:08 +0000 |
parents | 0fd0a757072c |
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1:0fd0a757072c | 2:d2ac1f5c05ed |
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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> |