fred-hutch-innovation-lab/proseg_xenium_nextflow is a bioinformatics pipeline that ...
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.
Now, you can run the pipeline using:
nextflow run fred-hutch-innovation-lab/proseg_xenium_nextflow \
-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.
fred-hutch-innovation-lab/proseg_xenium_nextflow was originally written by derrik.gratz.
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.
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.