marchoeppner / ngs-qc

QC tools for new sequencing runs (FastQC, FastQ Screen, MultiQC Report)

ngs-qc

QC tools for new sequencing runs (FastQC, FastQ Screen, MultiQC Report)

Setup instructions

This pipeline retrieves project-specific information from the CCGA Order tool. Make sure the environment variable "LIMS_TOKEN" is set to the authetication token for the order tool.

Usage instructions

This pipeline is currently configured to run on the IKMB DX Cluster. To start the pipeline, you need:

• singularity
• nextflow

Both of these should be available automatically.

The basic syntax is as follows:

nextflow run ikmb/ngs-qc --folder /mnt/demux/illumina/<PROJECT>

This will traverse all the project folders and produce both a global run statistic from the bcl2fastq stats file as well as per-library metrics on sequence quality and possible contaminations, separated by project name.

By default, the results are written to the folder "results", created in the place where the pipeline is launched from. Alternatively, you may specify --outdir /some/outdir to generate the results elsewhere. If you point --outdir to the same folder as the demuxed run, the QC reports should be correctly sorted into the respective project directories.

nextflow run ikmb/ngs-qc --folder /mnt/demux/illumina/<PROJECT> --outdir /mnt/demux/illumina/<PROJECT>

Other options

--sub_qc [ default = true ]

Enable or disable sub pipelines.

--metadata [ default = true ]

Generate a metadata sheet in XLSX format. Can be set to false to skip.