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https://github.com/mskcc/loki

Workflow for handling CNV events
https://github.com/mskcc/loki

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Workflow for handling CNV events

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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.



![Loki graph](docs/images/Loki.png)



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).