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SneakerNetInput.md

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SneakerNet Input folder

Scripts

Usually you can run this script to import a MiSeq run:

SneakerNet.roRun.pl path/to/dir -o SneakerNetDir --createsamplesheet

where SneakerNetDir is a properly formatted directory for SneakerNet. For this particular script, fastq filenames must be in the format of _R1_/_R2_ instead of _1/_2.

Building from scratch

Or you can just build the directory without an automated script.

Required

*.fastq.gz

Raw read files, both R1 and R2 if available. Single end raw reads are okay too.

SampleSheet.csv and/or samples.tsv

See below for samples.tsv, if SampleSheet.csv is not found.

Recommended

samples.tsv

This file can be created from SampleSheet.csv by the plugin sn_parseSampleSheet.pl, from SneakerNet.roRun.pl --createsamplesheet, from sn_createSampleSheet.pl, or manually. It has three columns, separated by tab:

  • sample - Name for a sample
  • info - semicolon-delimited information. Keys are separated by an equals sign. For example: taxon=Vibrio;route=calcEngine means that the taxon is Vibrio and the ultimate destination for the files are in calcEngine. Vibrio is the key for the taxon in config/taxonProperties.conf and will not have meaning if there is no entry.
  • filenames - semicolon-delimited fastq files. For example, ./2018AW-0585_S318_L001_R1_001.fastq.gz;./2018AW-0585_S318_L001_R2_001.fastq.gz

snok.txt

This file stands for "SneakerNet Okay" which is an indicator that the run is ready to be analyzed. The file is only necessary if a custom script needs to know whether the run is ready to be analyzed in an automated fashion. At minimum, snok.txt is a zero-byte file.

However, this file can also have content in a key/value format separated by an equals sign. The values can be comma-separated. Whitespace around each value is ignored. For example:

emails   = [email protected], [email protected], [email protected]
workflow = default
additional_plugins = sn_cleanup.pl

The current keys are emails and workflow. Emails describe where to send reports to, in addition to those in config/emails.conf. Workflow describes the set of plugins, and their order. Workflows are further described in config/plugins.conf.

Also in this example, files will be cleaned up in the SN run as described in the sn_cleanup.pl plugin. additional_plugins can have multiple plugins, comma separated.

Optional

These files are found in the Illumina run directory although they are optional.

  • CompletedJobInfo.xml
  • config.xml
  • QC/CompletedJobInfo.xml
  • QC/GenerateFASTQRunStatistics.xml
  • QC/RunInfo.xml
  • QC/runParameters.xml
  • QC/InterOp/ - this directory contains other files from the default Illumina run directory