Introduction

nf-core/createpanelrefs is a bioinformatics helper pipeline that will help in creating panel of normals and other models.

1. Read QC (FastQC)
2. Build Panel of Normals for CNVKIT
3. Build ploidy and cnv calling models for GATK's germlinecnvcaller workflow
4. Build Panel of Normals for GENS
5. Build Panel of Normals for Mutect2
6. Present QC for raw reads (MultiQC)

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,bam,bai,cram,crai
sample1,sample1.bam,sample1.bai,,
sample2,sample2.bam,,,
sample3,sample3.bam,sample3.bai,,
sample4,sample4.bam,,,

Each row in the samplesheet represents an alignment file, and it is important that you provide the files in the right format for the analysis you want to run.

Tool	Alignment format
cnvkit	bam
germlinecnvcaller	bam or cram or a mix of both

Now, you can run the pipeline using:

nextflow run nf-core/createpanelrefs \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --tools <cnvkit/germlinecnvcaller> \
   --genome GATK.GRCh38 \
   --outdir <OUTDIR>

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/createpanelrefs was originally written by @maxulysse. @marrip contributed in the idea that started it all. @matthdsm and @FriederikeHanssen contributed in the actual design. @ramprasadn's interest was the final push that led to the creation.

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

• @jfy133
• @JoseEspinosa

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 #createpanelrefs 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.