Mercurial > repos > jpayne > snp_pipeline

comparison 2_call_sites.xml @ 58:d53281e6edae

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planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents e90a783a4e8b
children 49d672730d3e
comparison
equal deleted inserted replaced
57:d3095ad12f24 58:d53281e6edae
1 <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10"> 1 <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10">
2 <description>of high-confidence SNPs, or lookup cached sitecall</description> 2 <description>of high-confidence SNPs, or lookup cached sitecall</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3.5">bowtie2</requirement> 4 <container type="docker">quay.io/biocontainers/mulled-v2-e518cb713b80020daa244e2ce559c37edb42dcde:5cb90165033bd74a97d0a807f439cf4b1aaabb89-0</container>
5 <requirement type="package" version="2.4.5">bowtie2</requirement>
5 <requirement type="package" version="1.9">samtools</requirement> 6 <requirement type="package" version="1.9">samtools</requirement>
6 <requirement type="package" version="1.0.6">bzip2</requirement> 7 <requirement type="package" version="1.0.8">bzip2</requirement>
7 <requirement type="package">picard</requirement> 8 <requirement type="package" version="2.27.4">picard</requirement>
8 <requirement type="package">varscan</requirement> 9 <requirement type="package" version="2.4.4">varscan</requirement>
9 <requirement type="package" version="1.9.134">boto3</requirement> 10 <requirement type="package" version="1.9.134">boto3</requirement>
10 <requirement type="package" version="3.6.8">python</requirement> 11 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
11 </requirements> 12 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 14 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
14 python $__tool_directory__/snp-cache.py snp_sitecalls 15 python $__tool_directory__/snp-cache.py snp_sitecalls
15 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)" 16 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"