Introduction

nf-cmgg/sampletracking is a bioinformatics pipeline that performs sampletracking on sequencing samples. The pipeline does this by crosschecking SNP fingerprints and by checking if the expected sex matches the real sex of the sample.

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,pool,sex,sample_bam,sample_bam_index,snp_bam,snp_bam_index
SAMPLE1,POOL1,F,SAMPLE1.bam,SAMPLE1.bam.bai,SAMPLE1_snp.cram,SAMPLE2_snp.cram.crai

Each row represents a sample annotated with the pool it was sequenced in and the expected sex of this sample. It also needs a BAM/CRAM file with the sample data and (optionally) a FASTQ/BAM/CRAM file with SNP tracking data for the sample. Crosschecking fingerprints will be skipped when no SNP tracking data is provided.

Now, you can run the pipeline using:

nextflow run nf-cmgg/sampletracking \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --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.

Credits

nf-cmgg/sampletracking was originally written by @matthdsm.

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

• @nvnieuwk

Contributions and Support

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

Citations

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.