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Functional Observation of RNA Transcriptome Elements/Expression

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// repository documentation

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# FORTE

## Introduction

**mskcc/forte** is a best-practice analysis pipeline for bulk RNAseq.

- **F**unctional
- **O**bservation of
- **R**NA
- **T**ranscriptome
- **E**lements/**E**xpression

### Features

1. Read pre-processing
   1. Trimming
   2. UMI extraction and deduplication
2. Alignment
3. Transcript quantification
4. Fusion calling and annotation
5. FASTQ and BAM QC
6. Fillouts

## Quick Start

1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)

2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.

3. Clone the pipeline repository and test it on a minimal dataset with the following steps:

```bash
   nextflow run /path/to/clonedrepo/main.nf -profile test,singularity --outdir <OUTDIR>
   ```

Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.

## 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.
:::

Now, you can run the pipeline using:

```bash
nextflow run /path/to/clonedrepo/main.nf \
  --input samplesheet.csv \
  --outdir <OUTDIR> \
  --genome GRCh37 \
  -profile singularity
```

:::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).
:::

For more details and further functionality, please refer to the [usage documentation](docs/usage.md).

## Pipeline output

For more details about the output files and reports, please refer to the
[output documentation](docs/output.md).

## Credits

mskcc/forte was originally written by Anne Marie Noronha <noronhaa@mskcc.org>.

We thank the following people for their extensive assistance in the development of this pipeline:

- Allison Richards <richara4@mskcc.org>
- Alexandria Pinto <pintoa1@mskcc.org>
- Yixiao Gong <gongy@mskcc.org>

We also thank the following contributors:

- Sam Tischfield <tischfis@mskcc.org>
- Martina Bradic <bradicm@mskcc.org>
- Jun Woo <wooh@mskcc.org>
- Mark Donoghue <donoghum@mskcc.org>
- Helen Won

## 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.

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](https://dx.doi.org/10.1038/s41587-020-0439-x).

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