Taxonomic profiling pipeline

Raw reads mOTUs and taxonomic classification pipeline.

Pipeline summary

The containerised pipeline for profiling shotgun metagenomic data is derived from the MGnify pipeline raw-reads analyses, a well-established resource used for analyzing microbiome data. Results of chosen studies are available on FTP.

Key components:

• Quality control and decontamination
• rRNA and ncRNA detection using Rfam database
• Taxonomic classification of SSU and LSU regions based on SILVA database
• Abundance analysis of mOTUs (Metagenomic Operational Taxonomic Units)

The pipeline is implemented in Nextflow and needs as second dependency either Docker or Singularity. All databases are automatically downloaded by Nextflow.

Quick Start

1. Install Nextflow

2. Install any of Docker or Singularity.

3. Download the pipeline and test it on a minimal dataset.

Run examples

Add your own profile to nextflow.config file including all inputs

Basic run

nextflow run EBI-Metagenomics/motus_pipeline \
-profile <choose profile> \
--mode <single/paired> \
--single_end  / --paired_end_forward --paired_end_reverse <path with fastq file/s>\
--sample_name <accession/name>

Using the fetch tool to download the reads

nextflow run EBI-Metagenomics/motus_pipeline \
-profile local \
--mode single \
--sample_name test
--reads_accession ERR4387386

Local Single End run

nextflow run EBI-Metagenomics/motus_pipeline \
-profile local \
--mode single \
--single_end my_reads/raw/test.fastq.gz \
--sample_name test

Local Paired Ends run

nextflow run EBI-Metagenomics/motus_pipeline \
-profile local \
--mode paired \
--paired_end_forward my_reads/raw/test_1.fastq.gz \
--paired_end_reverse my_reads/raw/test_2.fastq.gz \
--sample_name test

Development

Install development tools (including pre-commit hooks to run Black code formatting).

pip install -r requirements-dev.txt
pre-commit install

Code style

Use Black, this tool is configured if you install the pre-commit tools as above.

To manually run them: black .

Testing

The pipeline unit test are executed using nf-test.

To run the nextflow unit tests the databases have to downloaded manually, we are working to improve this.

nf-test test tests/*