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SYNOPSIS

sn_report.pl

Creates an HTML report for a SneakerNet run. Usually, this is the second-to-last plugin to run, right before the email plugin.

Software requirements

Algorithm

key value pairs

Reads all properties in SneakerNet/properties.txt, which has three columns: plugin, key, value. If a duplicate plugin/key combination is found, then the latest value is used.

Properties are recorded into SneakerNet/properties.txt from other plugins. With the perl plugins, these are recorded using SneakerNet::recordProperties() which is documented via perldoc lib/perl5/SneakerNet.pm.

Warnings

If the plugin key is warnings, then it will display any warnings at the top of the report.

Errors

If the plugin key is errors, then it will display any errors at the top of the report.

tables

If the value has a suffix .csv or .tsv, then the corresponding table is converted to HTML and included in the report. All other key/value combinations are included in the HTML report, under their corresponding plugins.

images

For this plugin version >= 2.7

If the value has a suffix .png or .gif, then the corresponding file path will be converted to base64 and embedded in the HTML report.

Outputs

HTML report

emoji output

This script itself outputs a table and is therefore converted to a table in the HTML report. The table has columns:

  • sample - sample name
  • emoji - reflective of the score. Happiest emojis reflect 100%.
    • As of v0.15, emoticons range from 😃 (best), 🤨, 😬, and 😱 (worst).
  • score - a percentage, starting from 100. Each item under the failure_code column subtracts an equal percentage from 100%. These possible failures are shown as columns in the passfail plugin. If there are three possible items, then each penalty is 33%. By default in SneakerNet version 0.10, there are three possible items: coverage, quality, and kraken.
  • qual - quality scores of R1 and R2, separated by space.
  • cov - genome coverages of R1 and R2, separated by space.
  • taxon - the calculated taxon. The calculated taxon is, in priority order: the taxon listed on the sample spreadsheet, guessed from Kraken, pattern matching on the filename, and lastly "UNKNOWN". For example, if the taxon is specified on the sample spreadsheet, it will be used and not overwritten.