nf-cmgg/report is a bioinformatics pipeline that will do some common reporting whitin our institute.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
- Extract and filter reads from input CRAM files (SAMtools)
- Merge overlapping paired end reads (pear)
- Combine PEAR output and singletons (mergereads)
- Count the reads at location of mutation (hotcount)
| Tool | Version |
|---|---|
| SAMtools | 1.21 |
| PEAR | 0.9.6 |
| hotcount | 0.0.0 |
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,cram,crai,design
CONTROL_REP1,AEG588A1_S1_L002_R1_001.cram,AEG588A1_S1_L002_R2_001.crai,FamCanc_v2Each row represents a sample name, the cram file associated with the sample, the crai file of the sample, the design used for the sample.
Now, you can run the pipeline using:
nextflow run nf-cmgg/report -profile <docker/singularity> --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.
nf-cmgg/report was originally written by Tuur-ds,nvnieuwk.
We thank the following people for their extensive assistance in the development of this pipeline:
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.