qbic-pipelines/intersectvcfs
README
Introduction
qbic-pipelines/intersectvcfs is a bioinformatics pipeline that ...
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.
Now, you can run the pipeline using:
nextflow run qbic-pipelines/intersectvcfs \
-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
qbic-pipelines/intersectvcfs was originally written by FriederikeHanssen.
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.
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.
qbic-pipelines/intersectvcfs pipeline parameters
Intersects Strelka2 and Mutect2 VCF files
Total Parameters: 28
Input/output options
4 parameters
Institutional config options
6 parameters
Max job request options
3 parameters
Generic options
15 parameters
Launch Pipeline
Run this pipeline using Seqera on top of your own compute.