https://github.com/mskcc/loki
Workflow for handling CNV events
https://github.com/mskcc/loki
Last synced: 4 months ago
JSON representation
Workflow for handling CNV events
- Host: GitHub
- URL: https://github.com/mskcc/loki
- Owner: mskcc
- License: mit
- Created: 2023-11-13T22:48:11.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2025-02-06T21:30:21.000Z (over 1 year ago)
- Last Synced: 2026-01-28T07:49:33.519Z (5 months ago)
- Language: Nextflow
- Size: 2.16 MB
- Stars: 2
- Watchers: 11
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATIONS.md
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## Introduction
**mskcc/loki** is a bioinformatics pipeline that calculates Copy Number Variation (CNV) mutation data from a Tumor/Normal Bam pair. The pipeline uses MSKCC Facets/Facets-suite and calculates pileups using MKSCC Htstools.
1. Calculate pileups ([`htstools`](https://github.com/mskcc/htstools/releases/tag/snp_pileup_0.1.1))
2. Calculate CNV results ([`Facets-suite`](https://github.com/mskcc/facets-suite/releases/tag/2.0.9))
## Usage
> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
#### Running nextflow @ MSKCC
If you are runnning this pipeline on a MSKCC cluster you need to make sure nextflow is properly configured for the HPC envirornment:
```bash
module load java/jdk-17.0.8
module load singularity/3.7.1
export PATH=$PATH:/path/to/nextflow/binary
export SINGULARITY_TMPDIR=/path/to/network/storage/for/singularity/tmp/files
export NXF_SINGULARITY_CACHEDIR=/path/to/network/storage/for/singularity/cache
```
### Running the pipeline
First, prepare a samplesheet with your input data that looks as follows:
`samplesheet.csv`:
```csv
pairId,tumorBam,normalBam,assay,normalType,bedFile
pair_sample,/bam/path/foo_tumor.rg.md.abra.printreads.bam,/bam/path/foo_normal.rg.md.abra.printreads.bam,IMPACT505,MATCHED,NONE
```
> [!IMPORTANT]
> Make sure the bams have an index file associated with it either file.bam.bai or file.bai should work
Now, you can run the pipeline using:
```bash
nextflow run main.nf \
-profile singularity,test_juno \
--input samplesheet.csv \
--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](https://nf-co.re/usage/configuration#custom-configuration-files).
## Credits
mskcc/loki was originally written by Nikhil Kumar [@nikhil](https://github.com/nikhil).
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
## Citations
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/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](https://dx.doi.org/10.1038/s41587-020-0439-x).