Nextflow wrapper for spotyping process.

Pre-requisites

• Conda
  • Nextflow
  • Spotyping

It is expected that you already have setup conda environment with the required packages.

conda create -c bioconda -n spotyping spotyping nextflow

Activate the environment

conda activate spotyping

Usage

nextflow run https://github.com/nf-modules/spotyping

Options

• query

By default, the spotyping queries the databaset. To suppress this behavior, you can use the query parameter.

nextflow run https://github.com/nf-modules/spotyping --query false

• filePattern

By default, the process assumes the files to follow the *_{R1,R2}.fastq.gz pattern, which could be customized using this option

nextflow run https://github.com/nf-modules/spotyping --filePattern './*_{1,2}.fastq.gz'

• resultsDir

By default, it stores the result files locally inside the results directory.

nextflow run https://github.com/nf-modules/spotyping --resultsDir /path/to/custom/resultsDir

• saveMode

By default, the pipeline publishes the results in the resultsDir by copying the relevant output.

You can update this behavior by simply specifying the alternative such as move or link etc.

nextflow run https://github.com/nf-modules/spotyping --saveMode move

For more information please refer Nextflow documentation

Cleanup space

NOTE: Once the analysis is completed and the expected results have been completed you can delete the work directory.

Customizing the script

The sole purpose of process wrappers in nf-modules is to keep the code small, clean and hackable with some basic knowledge of nextflow scripting.

If you have specific requirements, you are encouraged to fork/clone and update your version to accomodate your needs.

Contribution

Contribution, in all forms, is most welcome!