Introduction
nf-core/seqinspector is a bioinformatics pipeline that …
Usage
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
:
Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
Now, you can run the pipeline using:
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/seqinspector was originally written by the Swedish @NationalGenomicsInfrastructure.
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 #seqinspector
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.