staramrnf - 0.2.0

staramrnf 0.2.0 - 2024-09-20

DESCRIPTION

The pipeline has been modified to accept an input (samplesheet) with an optional sample_name column. The goal of the sample_name is to allow for IRIDA-Next users to modify their output filenames and sample names. Previously, all files and samples were named using the IRIDA-Next ID (for which users do not chose). This modification will not impact the running locally of staramrnf because if sample_name column is absent (as was the case prior to the release) then the sample column will behave as it had previously.

CHANGED

• sample_name special characters will be replaced with "_"
• If no sample_name is supplied in the column sample will be used
• To avoid repeat values for sample_name all sample_name values will be suffixed with the sample value. Which is a unique value.

- Nextflow
Published by sgsutcliffe over 1 year ago

staramrnf - 0.1.0

staramrnf 0.1.0 - 2024-08-14

Initial release of staramrnf, or staramr nextflow pipeline, is a nextflow wrapper of staramr.

staramr (AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The `star|instaramr` indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases.

staramrnf follows the nf-core pipeline file structure and used the nf-core template

- Nextflow
Published by sgsutcliffe over 1 year ago