aladdin-miqScoreShotgun

Nextflow pipeline that calculates MIQ Shotgun score. Compatible with Compatible with Aladdin Bioinformatics Platform.. This is essentially a Nextflow wrapper that runs the code at miqScoreShotgunPublic repo. Please refer to the original repo for more information on the source code.

Adaptation for Aladdin

In order to be compatible with Aladdin platform, this pipeline requires a design CSV file as input. The design CSV file must have the following format

group,sample,read_1,read_2
,Sample1,s3://mybucket/this_is_s1_R1.fastq.gz,s3://mybucket/this_is_s1_R2.fastq.gz

Because the miqScoreShotgunPublic code only supports one sample at a time, only the 1st row after the header is recognized.

How to run the pipeline

Prerequisites

• Nextflow version 20.07.1 or later
• Docker if using docker profile
• Permissions to AWS S3 and Batch resources if using awsbacth profile

Using Docker

nextflow run Zymo-Research/aladdin-miqScoreShotgun \
	--profile docker \
	--design "<path to design CSV file>"

Using AWS Batch

nextflow run Zymo-Research/aladdin-miqScoreShotgun \
	-profile awsbatch \
	--design "<path to design CSV file>" \
	-work-dir "<work dir on S3>" \
	--awsqueue "<SQS ARN>" \
	--outdir "<output dir on S3>" \

The parameters --awsqueue, -work-dir, and --outdir are required when running on AWS Batch, the latter two must be directories on S3.

Report and Documentation

Sample report

A sample report this pipeline produces can be found here.

Report documentation

A documentation explaining how to understand the report can be found here.