Introduction

mskcc/odin is a bioinformatics pipeline that performs variant analysis on a pair of bams. The output is an annotated maf that is properly filtered and annotated.

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.

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:

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:

pairId,tumorBam,normalBam,assay,normalType,bedFile
pair_id,tumor.bam,normal.bam,assay,normalType,optional:regions.bed

Each row represents a pair of bam files and bait set.

For optional bed file, you can either enter a bed file leave it bank and one will be generated using covered intervals. To leave the field blank you can use any of these options:

pair_id,tumor.bam,normal.bam,assay,normalType,NONE
pair_id,tumor.bam,normal.bam,assay,normalType,null
pair_id,tumor.bam,normal.bam,assay,normalType,

Now, you can run the pipeline using:

nextflow run

nextflow run main.nf \
   -profile singularity,test_juno \
   --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.

Credits

mskcc/odin was originally written by C. Allan Bolipata.

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

• Nikhil (@nikhil)

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.

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.