SneakerNet is a set of plugins. Each plugin runs a distinct analysis on a MiSeq run and accepts specific flags when it is run. Therefore, any given plugin can run independently of the others (aside from any prerequisite files, e.g., genome assemblies from a previous plugin).
Quick table of contents:
SneakerNet workflows define a particular order for the plugins to run. They help resolve dependencies like ensuring that genome assemblies are present before analyzed or enforcing that a report is generated only after all plugins have created their outputs.
Workflows are defined in plugins.conf.
The exact order of plugins for all workflows can be found by running the command SneakerNet.checkdeps.pl --list.
To make your own custuom workflow, edit the file under config/plugins.conf.
Plugins are run in the order specified for any given workflow. For example:
default = pluginA.pl, pluginB.pl, pluginZ.pl
In this example, in the default workflow,
if pluginB has a dependency on pluginZ, you might want to change the order
so that pluginB runs last.
default = pluginA.pl, pluginZ.pl, pluginB.pl
This workflow runs most plugins and assumes that you have some flavor of Illumina (MiSeq, HiSeq, MiniSeq).
This workflow runs plugins designed for ion torrent.
For metagenomics runs.
For assembly-only runs (ie, only assemblies and not raw reads in the folder).
For running the SARS-CoV-2 workflow. Plugin(s) are prefixed with sn_sars_.
Workflows in SneakerNet are defined by which plugins are run and in which order.
You can run SneakerNet.checkdeps.pl --list to see which plugins are run and in which order, for any workflow.
This script pulls from config/plugins.conf.
Below is the output for SneakerNet version 0.11.2.
By default, only default will be run in a SneakerNet analysis, but other workflows are available.
The pseudo-workflow all is an alphabetical listing of all available plugins.
$ SneakerNet.checkdeps.pl --list
all
addReadMetrics.pl, assembleAll.pl, baseBalance.pl, emailWhoever.pl, sn_assemblyWorkflow_init.pl, sn_crypto_assembleAll.pl, sn_crypto_gp60.pl, sn_detectContamination-kraken.pl, sn_detectContamination-mlst.pl, sn_detectContamination.pl, sn_helloWorld.pl, sn_helloWorld.py, sn_helloWorld.sh, sn_immediateStatus.pl, sn_iontorrent_assembleAll.pl, sn_kraken-metagenomics.pl, sn_kraken.pl, sn_mlst.pl, sn_mlst-wg.pl, sn_parseSampleSheet.pl, sn_passfail.pl, sn_report.pl, sn_SalmID.pl, sn_saveFailedGenomes.pl, sn_staramr.pl, transferFilesToRemoteComputers.pl
assembly
sn_assemblyWorkflow_init.pl, sn_mlst.pl, sn_staramr.pl, sn_passfail.pl, sn_kraken.pl, sn_detectContamination-kraken.pl, sn_report.pl, emailWhoever.pl
cryptosporidium
sn_parseSampleSheet.pl, addReadMetrics.pl, sn_crypto_assembleAll.pl, sn_mlst.pl, sn_kraken.pl, sn_detectContamination-kraken.pl, sn_passfail.pl, transferFilesToRemoteComputers.pl, emailWhoever.pl
default
sn_parseSampleSheet.pl, addReadMetrics.pl, assembleAll.pl, sn_mlst.pl, sn_kraken.pl, sn_detectContamination-kraken.pl, sn_detectContamination-mlst.pl, baseBalance.pl, sn_staramr.pl, sn_passfail.pl, transferFilesToRemoteComputers.pl, sn_report.pl, emailWhoever.pl
iontorrent
addReadMetrics.pl, sn_iontorrent_assembleAll.pl, sn_mlst.pl, sn_kraken.pl, sn_detectContamination-kraken.pl, sn_passfail.pl, sn_staramr.pl, transferFilesToRemoteComputers.pl, emailWhoever.pl
metagenomics
sn_parseSampleSheet.pl, addReadMetrics.pl, sn_kraken.pl, sn_kraken-metagenomics.pl, sn_passfail.pl, sn_report.pl
graph TD
A(reads) -->|sn_parseSampleSheet.pl| B(raw reads, samples.tsv)
B -->|addReadMetrics.pl| C(read metrics)
B -->|assembleAll.pl| D(assembly, assembly metrics)
D -->|sn_mlst.pl| E(7-gene MLST results)
B -->|sn_kraken.pl| F[Kraken results]
F -->|sn_detectContamination-kraken.pl| G(Kraken contamination report)
B -->|sn_detectContamination-mlst.pl| H(MLST contamination report)
B -->|baseBalance.pl| I(base balance report)
D -->|sn_staramr.pl| J(AMR results)
G -->|sn_passfail.pl| K(pass or fail results)
C -->K
D -->K
K -->|transferFilesToRemoteComputers.pl| L(transfer report)
K -->|sn_report.pl| M(sneakernet report)
M -->|emailWhoever.pl| N(email with SN report)
B -->M
C -->M
D -->M
E -->M
F -->M
G -->M
H -->M
I -->M
J -->M
graph TD
A(assemblies) --> |sn_assemblyWorkflow_init.pl| B(Copies of assemblies)
A --> |sn_assemblyWorkflow_init.pl| C(Gene predictions)
B --> I(genome metrics)
C --> I
B --> |sn_mlst.pl| D(Sequence types)
B --> |sn_staramr.pl| E(AMR profiles)
B --> |sn_kraken.pl| F(Kraken results)
F --> |sn_detectContamination-kraken.pl| G(Contamination results)
G --> |sn_passfail.pl| H(passfail)
I --> |sn_passfail.pl| H
H --> |sn_report.pl| J(SN report)
F --> J
G --> J
D --> J
E --> J
I --> J
Each plugin can accept the following options. The first positional parameter must be the SneakerNet run.
| Flag | Default value | description |
|---|---|---|
--help |
generate a help menu | |
--numcpus |
1 | Parallelization |
--debug |
generate more messages or any other debugging | |
--tempdir |
automatically generated, e.g., with File::Temp or mktemp |
Where temporary files are located |
--force |
This is loosely defined but can be used for many things like overwriting output files | |
--version |
Print a version in the format of X.Y or X.Y.Z | |
--citation |
Print a citation statement. | |
--check-dependencies |
check all executable dependencies. Print executable dependencies to stdout and version information to stderr. Run SneakerNet.checkdeps.pl to check dependencies on all plugins. |
Except for the legacy plugins, all plugins are prefixed with sn_.
The plugins are not specific to any one language, although the majority
are in Perl.
Contributions are welcome for the following plugin documents.
| Plugin | description |
|---|---|
| sn_SalmID.pl | Salmonella subspecies identification |
| sn_staramr.pl | staramr antimicrobial resistance determinant analysis |
| sn_passfail.pl | Table of pass/fail for each sample |
| sn_iontorrent_assembleAll.pl | Assembly for ion torrent data |
| addReadMetrics.pl | Raw read metrics |
| sn_helloWorld.pl | Example plugin in Perl |
| sn_helloWorld.sh | Example plugin in Bash |
| sn_helloWorld.py | Example plugin in Python |
| baseBalance.pl | Dividing all As by Ts and all Cs by Gs to see if we get a ratio of 1 for each |
| sn_mlst.pl | Runs 7-gene MLST on assemblies |
| sn_mlst-wg.pl | Runs whole-genome MLST on assemblies |
| transferFilesToRemoteComputers.pl | Transfers files to a remote computer |
| sn_detectContamination.pl | Detects potential contamination by kmer counting |
| emailWhoever.pl | Emails all results |
| sn_detectContamination-mlst.pl | Runs 7-gene MLST on raw reads, checking for abnormal number of alleles |
| sn_iontorrent_parseSampleSheet.pl | Turns the sample sheet for ion torrent into SneakerNet format |
| sn_immediateStatus.pl | Emails an immediate report |
| guessTaxon.pl | Runs metagenomics classifier to guess the taxon for a sample |
| sn_kraken.pl | Runs metagenomics classifier on raw reads, or on assemblies if reads are not present. No secondary analysis is performed by this exact plugin. E.g., sn_detectContamination-kraken.pl. |
| sn_detectContamination-kraken.pl | Runs metagenomics classifier to guess the taxon for a sample and list at most a single major contaminant |
| sn_kraken-metagenomics.pl | Analyzes kraken results for a metagenomics sample |
| assembleAll.pl | Assembles Illumina data |
| sn_assemblyWorkflow_init.pl | For workflows that only have assembly data. Initializes the workflow so that other plugins can function properly. |
| sn_crypto_assembleAll.pl | Assembles Illumina data for Cryptosporidium |
| sn_crypto_gp60.pl | Provides the gp60 profile for Cryptosporidium |
| sn_parseSampleSheet.pl | Turns the sample sheet for Illumina into SneakerNet format |
| sn_report.pl | Creates an HTML report from all other plugins |
| sn_sarscov2_assembleAll.pl | Runs assembly for SARS-CoV-2 amplicon-based genomes |
| sn_assembleAll_reference.pl.md | Runs reference assembly |
| sn_saveFailedGenomes.pl | Saves genomes into the destination folder, into a QC_Fails subfolder |
| sn_cleanup.pl | Cleans intermediate files in a SN directory |
| sn_genotype.pl | Runs genotyping on samples, e.g., serogrouping |
| sn_genotype_escherichia.pl | Interprets genotyping on samples for Escherichia |