Mercurial > repos > kkonganti > cfsan_cronology
changeset 1:c6327baca625
"planemo upload"
author | kkonganti |
---|---|
date | Mon, 27 Nov 2023 14:18:16 -0500 |
parents | c8597e9e1a97 |
children | 408603fd75ca |
files | cfsan_cronology.xml |
diffstat | 1 files changed, 14 insertions(+), 12 deletions(-) [+] |
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--- a/cfsan_cronology.xml Mon Nov 27 12:37:44 2023 -0500 +++ b/cfsan_cronology.xml Mon Nov 27 14:18:16 2023 -0500 @@ -1,9 +1,9 @@ <tool id="cfsan_cronology" name="cronology" version="0.1.0"> <description>An automated workflow for Cronobacter isolate assembly, sequence typing and traceback.</description> <requirements> - <requirement type="package" version="23.04">nextflow</requirement> - <requirement type="package" version="1.0.0">micromamba</requirement> - <requirement type="package">graphviz</requirement> + <requirement type="package" version="23.04">nextflow</requirement> + <requirement type="package" version="1.0.0">micromamba</requirement> + <requirement type="package">graphviz</requirement> </requirements> <version_command>nextflow -version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -131,10 +131,8 @@ **Testing and Validation** 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 -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 -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 -our publication (https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full). All the original testing and validation was -done on the command line on the CFSAN Raven2 HPC Cluster. +and performs read quality control followed by de novo assembly, gene prediction and annotation, sequence typing and whole genome distance based clustering. +All the testing has been done on the command line on the CFSAN Raven2 HPC Cluster. ---- @@ -143,7 +141,7 @@ **Outputs** -The main output file is a: +The main output files are: :: @@ -152,6 +150,10 @@ work within Galaxy for the MultiQC report. Please download the file by clicking on the floppy icon and view it in your browser on your local desktop/workstation. You can export the tables and plots from the downloaded MultiQC report. + - Polished de novo assemblies (FASTA) for each sample. + - Genome annotations (GFF) for each sample. + - Whole genome distance based clustering tree (Newick). + - Additional metadata useful for uploading the Newick tree into iTOL. ]]></help> <citations> @@ -160,10 +162,10 @@ author = {Konganti, Kranti}, year = {2023}, month = {August}, - title = {cronology: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting}, - journal = {Frontiers in Microbiology}, - doi = {10.3389/fmicb.2023.1200983}, - url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full}} + title = {cronology: An automated workflow for Cronobacter isolate assembly, sequence typing and traceback}, + journal = {Unpublished}, + doi = {10.3389/fmicb.2023.120098312}, + url = {https://github.com/CFSAN-Biostatistics/cronology}} </citation> </citations> </tool>