[](https://github.com/nf-core/scge/actions?query=workflow%3A%22nf-core+CI%22) [](https://github.com/nf-core/scge/actions?query=workflow%3A%22nf-core+linting%22)[](https://nf-co.re/scge/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)

Introduction

nf-core/scge is a bioinformatics pipeline that ...

1. Runs tumor normal dragen
2. Get Indels
3. Get Transgene Junctions
4. Annotate Transgene Variants
5. Annotate sv, cnv, hard-filtered vcf
6. Makes vep to tsv file
7. Makes scge report

Usage

To run at dragen step, prepare a samplesheet with the following columns:

dragen_samplesheet.csv:

id,uid,sample_type,fastq_list,hotspot_file
tumor_sample_1,tumor_sample_1,tumor,/path/to/fastqlist,/path/to/hotspot_1
normal_sample,tumor_sample_1,normal,/path/to/fastqlist,/path/to/hotspot_1
tumor_sample_2,tumor_sample_2,tumor,/path/to/fastqlist,/path/to/hotspot_2
normal_sample,tumor_sample_2,normal,/path/to/fastqlist,/path/to/hotspot_2

The hotspot file is optional.

To run the pipeline from the analysis step: prepare a samplesheet with the following columns:

analysis_samplesheet.csv:

id,dragen_path,hotspot_file
sample1,/path/to/dragen_output/sample1,/path/to/hotspot_1
sample2,/path/to/dragen_output/sample2,/path/to/hotspot_2

Now, you can run the pipeline using:

nextflow run dhslab/nf-core-scge \
   -profile ris,<dragen2/dragen4/dragenaws> \
   --input /path/to/samplesheet \
   --outdir <OUTDIR>

Additional arguments:

--hotspot_bed - /path/to/hotspot.bed

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/scge was originally written by Nidhi.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #scge channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.