FORTE

Introduction

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

• Functional
• Observation of
• RNA
• Transcriptome
• Elements/Expression

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 (>=21.10.3)

2. Install any of Docker, Singularity (you can follow this tutorial), Podman, Shifter or Charliecloud for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).

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

   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 on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. :::

Now, you can run the pipeline using:

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. :::

For more details and further functionality, please refer to the usage documentation.

Pipeline output

For more details about the output files and reports, please refer to the output documentation.

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.

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.