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comparison cfsan_cronology.xml @ 1:c6327baca625

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 14:18:16 -0500
parents c8597e9e1a97
children 408603fd75ca
comparison
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0:c8597e9e1a97 1:c6327baca625
1 <tool id="cfsan_cronology" name="cronology" version="0.1.0"> 1 <tool id="cfsan_cronology" name="cronology" version="0.1.0">
2 <description>An automated workflow for Cronobacter isolate assembly, sequence typing and traceback.</description> 2 <description>An automated workflow for Cronobacter isolate assembly, sequence typing and traceback.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="23.04">nextflow</requirement> 4 <requirement type="package" version="23.04">nextflow</requirement>
5 <requirement type="package" version="1.0.0">micromamba</requirement> 5 <requirement type="package" version="1.0.0">micromamba</requirement>
6 <requirement type="package">graphviz</requirement> 6 <requirement type="package">graphviz</requirement>
7 </requirements> 7 </requirements>
8 <version_command>nextflow -version</version_command> 8 <version_command>nextflow -version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 mkdir -p cpipes-input || exit 1; 10 mkdir -p cpipes-input || exit 1;
11 pwd_path=\$(pwd); 11 pwd_path=\$(pwd);
129 .. class:: infomark 129 .. class:: infomark
130 130
131 **Testing and Validation** 131 **Testing and Validation**
132 132
133 The CPIPES - cronology Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input 133 The CPIPES - cronology Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input
134 and generates a MultiQC report in the final step. The pipeline has been tested on 2x300 bp MiSeq and 2x150 bp NextSeq simulated reads and has been shown to call multiple 134 and performs read quality control followed by de novo assembly, gene prediction and annotation, sequence typing and whole genome distance based clustering.
135 Salmonella serotypes with up to ~95% accuracy. The pipeline has also been tested on metagenomics data sets from Peach and Papaya outbreaks as discussed in 135 All the testing has been done on the command line on the CFSAN Raven2 HPC Cluster.
136 our publication (https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full). All the original testing and validation was
137 done on the command line on the CFSAN Raven2 HPC Cluster.
138 136
139 137
140 ---- 138 ----
141 139
142 .. class:: infomark 140 .. class:: infomark
143 141
144 **Outputs** 142 **Outputs**
145 143
146 The main output file is a: 144 The main output files are:
147 145
148 :: 146 ::
149 147
150 - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables. 148 - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables.
151 Please note that due to MultiQC customizations, the preview (eye icon) will not 149 Please note that due to MultiQC customizations, the preview (eye icon) will not
152 work within Galaxy for the MultiQC report. Please download the file by clicking 150 work within Galaxy for the MultiQC report. Please download the file by clicking
153 on the floppy icon and view it in your browser on your local desktop/workstation. 151 on the floppy icon and view it in your browser on your local desktop/workstation.
154 You can export the tables and plots from the downloaded MultiQC report. 152 You can export the tables and plots from the downloaded MultiQC report.
153 - Polished de novo assemblies (FASTA) for each sample.
154 - Genome annotations (GFF) for each sample.
155 - Whole genome distance based clustering tree (Newick).
156 - Additional metadata useful for uploading the Newick tree into iTOL.
155 157
156 ]]></help> 158 ]]></help>
157 <citations> 159 <citations>
158 <citation type="bibtex"> 160 <citation type="bibtex">
159 @article{cronology, 161 @article{cronology,
160 author = {Konganti, Kranti}, 162 author = {Konganti, Kranti},
161 year = {2023}, 163 year = {2023},
162 month = {August}, 164 month = {August},
163 title = {cronology: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting}, 165 title = {cronology: An automated workflow for Cronobacter isolate assembly, sequence typing and traceback},
164 journal = {Frontiers in Microbiology}, 166 journal = {Unpublished},
165 doi = {10.3389/fmicb.2023.1200983}, 167 doi = {10.3389/fmicb.2023.120098312},
166 url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full}} 168 url = {https://github.com/CFSAN-Biostatistics/cronology}}
167 </citation> 169 </citation>
168 </citations> 170 </citations>
169 </tool> 171 </tool>