Name: snakemake-amplicon-metagenomics
Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada
Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada
Description: Command line bioinformatics workflows, created with Snakemake workflow management tool.
Created: 2016-06-17 17:41:43.0
Updated: 2017-12-05 18:07:11.0
Pushed: 2017-07-05 19:20:18.0
Homepage: null
Size: 36
Language: Python
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This workflow describes a series of steps executed to get from raw fastq files, resulting from the amplicon sequencing of sample(s), to OTU table, describing the taxonomic determination summary for the analysed sample(s). It executes on Linux command line, using a Snakemake workflow management system.
For details on the workflow tools, their version, arguments used, and order of execution see Snakefile.
To check if the workflow will run correctly without executing the steps:
$ snakemake -np --configfile config.yaml
To execute the workflow:
$ snakemake --configfile config.yaml
Note: If you are not in the same directory as the Snakefile you will need the extra parameter --snakefile
with the path to the Snakefile
This worflow runs on Linux. To install this workflow, either locally or on a cluster, you will need to have the following requirements installed.
Download the latest release of this project:
https://github.com/AAFC-MBB/snakemake-amplicon-metagenomics/releases
OR
Check out this project (requires git):
$ git clone https://github.com/AAFC-MBB/snakemake-workflows.git
Automated test is located in snakemake-workflows/amplicon_workflow/test/. To run the test, first download the test data to snakemake-workflows/amplicon_workflow/test/data/ directory (see README in that directory for the instructions). Before you execute the test please note, that the test runs Snakefile with the test data and therefore uses the same output directory as a regular snakemake command (default is snakemake-workflows/amplicon_workflow/data). Therefore if you already have some input or intermetiate workflow execution data in your data directory and you would like to keep it - back it up.
Execute the tests:
$ ./test.sh -clean -run
For more information about Snakemake, visit their website: https://bitbucket.org/snakemake/snakemake/wiki/Home
See License file.