Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison cfsan_bettercallsal.xml @ 7:7d2019190ba2

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"planemo upload"
author kkonganti
date Tue, 06 Jun 2023 10:22:20 -0400
parents 83ed52d5af32
children 22165d5e5e0a
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6:83ed52d5af32 7:7d2019190ba2
146 .. class:: infomark 146 .. class:: infomark
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148 **Testing and Validation** 148 **Testing and Validation**
149 149
150 The CPIPES - bettercallsal Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input 150 The CPIPES - bettercallsal Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input
151 and generates a MultiQC report in the final step. The pipeline has been tested on 2x300 bp MiSeq and 2x150 bp NextSeq reads and has shown to call multiple 151 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 shown to call multiple
152 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 152 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
153 our preprint (https://www.biorxiv.org/content/10.1101/2023.04.06.535929v1.full). All the original testing and validation was 153 our preprint (https://www.biorxiv.org/content/10.1101/2023.04.06.535929v1.full). All the original testing and validation was
154 done on the command line on the CFSAN Raven2 HPC Cluster. 154 done on the command line on the CFSAN Raven2 HPC Cluster.
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159 .. class:: infomark 159 .. class:: infomark
160 160
161 **Outputs** 161 **Outputs**
162 162
163 The main output files are: 163 The main output file is a:
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165 :: 165 ::
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167 - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables. 167 - MultiQC Report: Contains a brief summary report including any serotyping and AMR result tables.
168 Please note that due to MultiQC customizations, the preview (eye icon) will not 168 Please note that due to MultiQC customizations, the preview (eye icon) will not