modules/staramr_search

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

amrplasmidmlstgenomics

https://github.com/nf-core/modules/[...]/modules/nf-core/staramr/search

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`results_xlsx`

`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

`summary_tsv`

`meta: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

`*_results/summary.tsv:file`

*_results/summary.tsv

`detailed_summary_tsv`

`meta:file`

*_results/detailed_summary.tsv

`*_results/detailed_summary.tsv:file`

*_results/detailed_summary.tsv

`resfinder_tsv`

`meta:file`

A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line.

*_results/resfinder.tsv

`*_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

`plasmidfinder_tsv`

`meta: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

`*_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

`mlst_tsv`

`meta:file`

A tabular file of each multi-locus sequence type (MLST) and it’s corresponding locus/alleles, one genome per line.

*_results/mlst.tsv

`*_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

`settings_txt`

`meta:file`

The command-line, database versions, and other settings used to run staramr.

*_results/settings.txt

`*_results/settings.txt:file`

The command-line, database versions, and other settings used to run staramr.

*_results/settings.txt

`pointfinder_tsv`

`meta: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

`*_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

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

staramr
Apache Software License

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.

github.com/phac-nml/staramr 10.3390/microorganisms10020292

modules/staramr_search

Description

Input

`meta:map`

`genome_fasta:file`

Output

`results_xlsx`

`meta:file`

`*_results/results.xlsx:file`

`summary_tsv`

`meta:file`

`*_results/summary.tsv:file`

`detailed_summary_tsv`

`meta:file`

`*_results/detailed_summary.tsv:file`

`resfinder_tsv`

`meta:file`

`*_results/resfinder.tsv:file`

`plasmidfinder_tsv`

`meta:file`

`*_results/plasmidfinder.tsv:file`

`mlst_tsv`

`meta:file`

`*_results/mlst.tsv:file`

`settings_txt`

`meta:file`

`*_results/settings.txt:file`

`pointfinder_tsv`

`meta:file`

`*_results/pointfinder.tsv:file`

`versions`

`versions.yml:file`

Tools

staramr
Apache Software License

maintainer

get in touch

modules/staramr_search

Description

Input

meta:map

genome_fasta:file

Output

results_xlsx

meta:file

*_results/results.xlsx:file

summary_tsv

meta:file

*_results/summary.tsv:file

detailed_summary_tsv

meta:file

*_results/detailed_summary.tsv:file

resfinder_tsv

meta:file

*_results/resfinder.tsv:file

plasmidfinder_tsv

meta:file

*_results/plasmidfinder.tsv:file

mlst_tsv

meta:file

*_results/mlst.tsv:file

settings_txt

meta:file

*_results/settings.txt:file

pointfinder_tsv

meta:file

*_results/pointfinder.tsv:file

versions

versions.yml:file

Tools

staramr Apache Software License

maintainer

get in touch

`meta:map`

`genome_fasta:file`

`results_xlsx`

`meta:file`

`*_results/results.xlsx:file`

`summary_tsv`

`meta:file`

`*_results/summary.tsv:file`

`detailed_summary_tsv`

`meta:file`

`*_results/detailed_summary.tsv:file`

`resfinder_tsv`

`meta:file`

`*_results/resfinder.tsv:file`

`plasmidfinder_tsv`

`meta:file`

`*_results/plasmidfinder.tsv:file`

`mlst_tsv`

`meta:file`

`*_results/mlst.tsv:file`

`settings_txt`

`meta:file`

`*_results/settings.txt:file`

`pointfinder_tsv`

`meta:file`

`*_results/pointfinder.tsv:file`

`versions`

`versions.yml:file`

staramr
Apache Software License