Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Prerequisites

1. Install Java.
2. Install nextflow.
3. Depending on your use case, install docker, or singularity. By using the docker or singularity nextflow profile, the pipeline can be run within the NOMAD docker container (also available on dockerhub, which contains all the required dependencies.

Try the pipeline

To test this pipeine, use the command below. The test profile will launch a pipeline run with a small dataset hosted on this repo (located in test_data/). The inputs for this profile are defined in conf/test.config.

How to run with singularity:

nextflow run kaitlinchaung/nomad-kmc3 \
    -profile test,singularity \
    -r main \
    -latest

How to run with docker:

nextflow run kaitlinchaung/nomad-kmc3 \
    -profile test,docker \
    -r main \
    -latest

Outputs

For each step, all output files are published in enumerated sub-directories. Here is the output file tree:

results/
├── module_1_10X_preprocessing
│   ├── step_1_umitools
│   ├── step_2_extract_cbc_umi
│   ├── step_3_concat_fastqs
│   └── step_4_dedup_cbc_umi
├── module_2_nomad_preprocessing
│   ├── step_1_fetch_anchors
│   ├── step_2_count_anchors
│   ├── step_3_stratify_anchors
│   └── step_4_get_abundant_anchors
├── module_3_nomad_statistics
│   └── step_1_compute_pvals
│   └── step_2_significant_anchors
└── pipeline_info

Citations

This pipeline uses code and infrastructure developed and maintained by the nf-core initative, and 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.