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FredHutch/interop-nf

InterOp QC Reporting - Nextflow
nextflowillumina
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  • Updated over 2 years ago
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READMELaunch Pipeline

README

Workflow used to generate QC metrics from the output of an Illumina sequencing run.

Run tests

codecov

Invoking the Workflow

The workflow can be run on the contents of an Illumina run folder with the following command:


runDirectory=<path to run directory>
reportsDirectory=<path to report output folder>

nextflow run FredHutch/InterOp-nf --runDir ${runDirectory} --reportsDir ${reportsDirectory}

The run folder must contain the InterOp/ folder and the RunInfo.xml and RunParameters.xml files.

Workflow output

View more info here.

Other information

Docker image used: https://github.com/FredHutch/docker-python-interop

Launch Pipeline

Run this pipeline using Seqera on top of your own compute.