Nextflow Registry | nf-core/staramr/search@0.0.0-6c4ed3a

nf-core/staramr/search @ 0.0.0-6c4ed3a

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

amr plasmid mlst genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @apetkau

Maintainers: @apetkau

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Add the following snippet to your workflow script to include this module.

include { STARAMR_SEARCH } from 'nf-core/staramr/search'

MIT License

Process

`Name`	`STARAMR_SEARCH`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`genome_fasta` file	Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids. `*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}`

Output 9 channels

#1 mlst_tsv tuple

`meta` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`
`*_results/mlst.tsv` file	A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line. `*_results/mlst.tsv`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 summary_tsv tuple

`meta` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`
`*_results/summary.tsv` file	A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. A series of descriptive statistics is also provided for each genome, as well as feedback for whether or not the genome passes several quality metrics and if not, feedback on why the genome fails. `*_results/summary.tsv`

#4 results_xlsx tuple

`meta` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`
`*_results/results.xlsx` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`

#5 settings_txt tuple

`meta` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`
`*_results/settings.txt` file	The command-line, database versions, and other settings used to run staramr. `*_results/settings.txt`

#6 resfinder_tsv tuple

`meta` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`
`*_results/resfinder.tsv` file	A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line. `*_results/resfinder.tsv`

#7 pointfinder_tsv tuple

`meta` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`
`*_results/pointfinder.tsv` file	An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line. `*_results/pointfinder.tsv`

#8 plasmidfinder_tsv tuple

`meta` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`
`*_results/plasmidfinder.tsv` file	A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line. `*_results/plasmidfinder.tsv`

#9 detailed_summary_tsv tuple

`meta` file	Excel spreadsheet containing summary of StarAMR results. `*_results/results.xlsx`
`*_results/detailed_summary.tsv` file	A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. A series of descriptive statistics is also provided for each genome, as well as feedback for whether or not the genome passes several quality metrics and if not, feedback on why the genome fails. `*_results/detailed_summary.tsv`

Tool	Description	Homepage
staramr	Scan genome contigs against the ResFinder and PointFinder databases. In order to use the PointFinder databases, you will have to add --pointfinder-organism ORGANISM to the ext.args options.	https://github.com/phac-nml/staramr