ParameterĪ text file containing sample names (one per line) to include from the analysisĪ text file containing sample names (one per line) to exclude from the analysisĪ database to query, if unavailable it will be downloaded to the path given by -ariba_dir
Use these parameters to specify which samples to include or exclude. The path to bactopia results to use as inputs FilenameĪ complete list of programs and versions used by each processĪ complete list of programs and versions formatted for MultiQCĭefine where the pipeline should find input data and save output data. FilenameĪt the end of each run, each of the versions.yml files are merged into the files below. Resource usage and estimate expected costs if using cloud platforms. These Nextflow reports provide great a great summary of your run. The Nextflow Trace report for the processĪ YAML formatted file with program versions The script executed by bash for the process The script Nextflow uses to stage/unstage files and queue processes based on given profile Logs ¶Įach process that is executed will have a logs folder containing helpful files for you to reviewĪn empty file used to designate the process startedĬontains both STDERR and STDOUT outputs from the process
FilenameĪll the assembled sequences that match the referenceĬontains the results from report.tsv in addition to synonymous mutationsĪ summary of the report created using ariba summaryĬontaines info on the versions of ARIBA and its dependenciesīelow are files that can assist you in understanding which parameters and program versions were used. FilenameĪ merged TSV file with ARIBA results from all samplesĪ merged CSV file created with ariba summaryīelow is a description of the per-sample results from ARIBA.
Results ¶ Top Level ¶īelow are results that are in the base directory. If executedįrom Bactopia, the ariba directory structure might be different, but the Ariba is available as a standalone Bactopia Tool, as well as from
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