RIVER- A Web Application to Run Nf-Core
Simply, I just want a web application. This is an all-in-one application similar to Google Drive, but more advanced. It allows me to select files and put them into a workflow obtained directly from GitHub. For example, rnaseq from nf-core. The web application allows me to run and monitor Nextflow jobs. Then, it puts the results back to Google Drive, where I can view the results. It is useful for sharing results with my team or external teams. I can develop pipelines independently. My data can be stored on the cloud for backup. It is a simple and standard procedure for bioinformatics analysis. But I have not found any solution that fits these requirements is EASY, FREE, OPEN-SOURCE
If you feel the same, RIVER may be your choice.
This blog post is intended for the general community, show cases only. I'll focus on the big picture rather than diving deep into technical details.
To use it, you can follow the below tutorial
Quick review
First, you can take a look at how it work first. In breif, it will allows the users to interact with S3 bucket, select inputs from S3 buckets, run and put back results to s3 that RIVER platform can visualize. After watching this, you are able to configure the RIVER platform as contributor, add your interested workflows and allow you to run tools
Get started
Your raw data should be uploaded to the platform. The fastq files are downloaded from the below url, then upload to the platform
The samplesheet.csv on test profile
sample,fastq_1,fastq_2
SAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz
SAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz
The samplesheet.csv on RIVER
sample,fastq_1,fastq_2
test,s3://genomics/demo/resources/fastq_files/sample1_R1.fastq.gz,s3://genomics/demo/resources/fastq_files/sample1_R2.fastq.gz