Mercurial > repos > jpayne > snp_pipeline

comparison 5_call_consensus.xml @ 62:d497922d6caa

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planemo upload
author jpayne
date Fri, 28 Jun 2024 00:26:24 -0400
parents 2af5e948dd5c
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61:2af5e948dd5c 62:d497922d6caa
1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10"> 1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
2 <description>for a sample, or lookup cached consensus SNP calls</description> 2 <description>for a sample, or lookup cached consensus SNP calls</description>
3 <requirements> 3 <requirements>
4 <!-- <container type="docker">quay.io/biocontainers/mulled-v2-fe715cf36e5a6063362b28e50f1f4a1a767770d5:8f94687b7d8826f1473b7e97df0cea2a960b35bf-0</container> --> 4 <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
5 <requirement type="package" version="1.0.8">bzip2</requirement> 5 <!-- <requirement type="package" version="1.0.8">bzip2</requirement>
6 <requirement type="package" version="2.2.1">snp-pipeline</requirement> 6 <requirement type="package" version="2.2.1">snp-pipeline</requirement>
7 <!-- <requirement type="package" version="1.9.134">boto3</requirement> --> 7 <requirement type="package" version="1.9.134">boto3</requirement> -->
8 <!-- <requirement type="package" version="3.6.8">python</requirement> --> 8 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
12 #set $identifier = $call_pileup.name.split(' ')[0] 12 #set $identifier = $call_pileup.name.split(' ')[0]