Mercurial > repos > jpayne > snp_pipeline

comparison 5_call_consensus.xml @ 61:2af5e948dd5c

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planemo upload
author jpayne
date Wed, 26 Jun 2024 00:58:54 -0400
parents 49d672730d3e
children d497922d6caa
comparison
equal deleted inserted replaced
60:0b0e3e4376a7 61:2af5e948dd5c
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/biocontainers/mulled-v2-fe715cf36e5a6063362b28e50f1f4a1a767770d5:8f94687b7d8826f1473b7e97df0cea2a960b35bf-0</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]