angelovangel/nextflow-fastp-shiny

a shiny frontend for the nextflow-fastp pipeline

nextflow-fastp-shiny

Background

This is a graphical user interface for the nextflow-fastp pipeline. The GUI is a Shiny app, which executes the underlying nextflow pipeline using processx calls. The pipeline itself retains all the flexibility of nextflow - it can be run in a conda environment or in a docker container, the data can be local or on an Amazon S3 bucket, the executor can be local, PBS, SLURM, AWS Batch...

Installation

All that is needed is nextflow and this shiny app. When the app is started for the first time, the angelovangel/nextflow-fastp pipeline is pulled from github and will be available under $HOME/.nextflow/assets/angelovangel/nextflow-fastp/.

To install the Shiny app:

git clone https://github.com/angelovangel/nextflow-fastp-shiny.git

#or, run directly from within an R session:
shiny::runGitHub('nextflow-fastp-shiny', 'angelovangel')

Note: the fastq folder has to be read-write accessible from the server where the app is running.

Usage

Select a folder containing fastq files using the Select fastq folder button and press Run nextflow-fastp pipeline. Results are written to the results-fastp folder within the fastq folder. The log files can be accessed by navigating to the fastq folder and running

cat .nextflow.log

Demo

Questions

The Shiny app and the nextflow pipeline are written and maintained by Angel Angelov, if you have questions or problems open an issue on github.

nextflow-fastp-shiny's Issues

keep processx running after closing browser window

The underlying processx (nextflow) has to keep running after closing the browser window. When it finishes, notify user (pass email as an input in shiny?).

add modal to collect project info, and pass it to nxf as --multiqc_config

Same as for the nextflow-bcl-shiny