Nazeeefa/summary-report-development

Prototype for a new type of summary report for flowcells, that is going to be real awesome!

summary-report-development

In this repository we will gather useful scripts that can be used in the process of developing new sequencing report at the SNP&Seq Technology platform.

This repository is not a repository for the final product and the final code. This is just a place to share scripts and ideas during the development process.

Pre-requisites

You need to:

• install Nextflow
• install Singularity (version > 2.6)
• Have a .genologicsrc file configured for the Clarity LIMS db you want to use

Downloading fastqc-screen database

Ideally we want to do this automatically, tough right now there are problems with internet-access from the fastq-screen containers, so this is a temporary workaround for that. Here's how you do it:

• Download fastqc-screen from here.
• Uncompress it
• Run fastq_screen --get_genomes

How to run the nextflow pipeline

Awesome, you're all set! Let's try generating reports for your favourite runfolder:

nextflow -c config/nextflow.config run main.nf \
          --runfolder ~/large_disk/180126_HSX122_0568_BHLFWLBBXX_small/ \
          --fastq_screen_db ~/large_disk/FastQ_Screen_Genomes/