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comparison cfsan_centriflaken.xml @ 50:2376aae1acab

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"planemo upload"
author kkonganti
date Tue, 12 Jul 2022 16:37:03 -0400
parents 8202a3cedcc4
children d2369dd16e78
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49:ae89554cbe71 50:2376aae1acab
4 <requirement type="package" version="22.04">nextflow</requirement> 4 <requirement type="package" version="22.04">nextflow</requirement>
5 <requirement type="package">graphviz</requirement> 5 <requirement type="package">graphviz</requirement>
6 </requirements> 6 </requirements>
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 mkdir -p cpipes-input; 9 mkdir -p cpipes-input || exit 1;
10 #for $key in $input.keys() 10 #for $key in $input.keys()
11 ln -sf '$input[$key]' './cpipes-input/$key'; 11 ln -sf '$input[$key]' './cpipes-input/$key';
12 #end for 12 #end for
13 pwd_path=\$(pwd); 13 pwd_path=\$(pwd);
14 $__tool_directory__/0.2.1/cpipes 14 $__tool_directory__/0.2.1/cpipes
112 112
113 .. class:: infomark 113 .. class:: infomark
114 114
115 **Purpose** 115 **Purpose**
116 116
117 Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These piepelines allow rapid 117 Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These pipelines allow rapid
118 and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking. It is based on methods described in our 118 and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking. It is based on methods described in our
119 previous publication (https://doi.org/10.1371/journal.pone.0245172). 119 previous publication ([Maguire *et al*, 2021](doi: https://doi.org/10.1371/journal.pone.0245172)).
120 120
121 ---- 121 ----
122 122
123 .. class:: infomark 123 .. class:: infomark
124 124
125 **Testing and Validation** 125 **Testing and Validation**
126 126
127 The CPIPES - Centriflaken Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads or long reads, generates MAGs and performs 127 The CPIPES - Centriflaken Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads or long reads, generates MAGs and performs
128 in silico-based analysis (i.e., virulence gene finding). Additionally, AMR gene finding analysis is also included in Centriflaken and performed on MAGs 128 in silico-based analysis (i.e., virulence gene finding). Additionally, AMR gene finding analysis is also included in Centriflaken and performed on MAGs
129 of interest. The final summary plots and tables can be downloaded from the provided MultiQC HTML report generated as part of the pipeline. 129 of interest. The final summary plots and tables can be downloaded from the provided MultiQC HTML report generated as part of the pipeline.
130 The Centriflaken pipeline was validated with data from our previously published method (Maguire et al, 2021) and was able to replicate the detection 130 The Centriflaken pipeline was validated with data from our previously published method ([Maguire *et al*, 2021](doi: https://doi.org/10.1371/journal.pone.0245172)) and was able to replicate the detection
131 and classification of STECs for each sample. We tested the pipeline with Nanopore data obtained from 21 additional enriched samples from 131 and classification of STECs for each sample. We tested the pipeline with Nanopore data obtained from 21 additional enriched samples from
132 irrigation water and was able to perform the entire precision metagenomics analysis in less than 5 hours for all of them. All the original testing and validation was 132 irrigation water and was able to perform the entire precision metagenomics analysis in less than 5 hours for all of them. All the original testing and validation was
133 done on the command line on the CFSAN Raven2 HPC Cluster. 133 done on the command line on the CFSAN Raven2 HPC Cluster.
134 134
135 135