chiamh/meta-microbeannotator-nf

Pathway analysis using microbeannotator for metagenomics and metatranscriptomics, using Nextflow

Nextflow microbeannotator pipeline

Pipeline and wrapper around using microbeannotator to compute pathway presence/absence in metagenomes or metatranscriptomes.

Introduction

Chiamh/meta-microbeannotator-nf is pipeline that extracts protein sequences from a set of metagenome/metatranscriptome annotations generated by Chiamh/meta-omics-nf (optional)
and performs pathway completeness analysis using microbeannotator v2.1.5

The pipeline is built using Nextflow DSL2 , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker containers (also compatible with Singularity) for ease of installation and computational reproducibility.

Input requirements

Either:

1. Absolute path to the folder containing the *_merged_panalign_annot.tsv AND *_merged_transl-search_annot.tsv specified with the --mgx_annotations and/or --mtx_annotations arguments.

• This will search the folder(s) recursively for the annotation files and run the pipeline on all of them.
  or:

2. Absolute path to the folder containing fasta files with protein sequences translated from ORFs found in metagenomes/metatranscriptomes using the -mgx_protein_seqs and/or -mtx_protein_seqs.

• These inputs are strictly for the "annotate" but not the "full" workflow!

Quick Start

1. Install Nextflow (>=21.04.0) and add the nextflow executable to your $PATH

2. Install Docker

3. Clone the pipeline and refer to the help message

   git clone https://github.com/Chiamh/meta-microbeannotator-nf
   
   nextflow run ./alignment-nf/meta-microbeannotator-nf --help
   

• Add a custom config file which contains the paths to various pre-installed databases. Refer to the awsbatch.config file in this repo for an example.
• Add a custom profile in the nextflow.config file, allowing you to specify the use of docker or singularity, and/or a task scheduler.

4. Make sure all helper scripts in alignment-nf/bin have execute permissions

   chmod +x ./meta-microbeannotator-nf/bin/*
   

5. (A): Run the pipeline (full workflow)

   nextflow run ./meta-microbeannotator-nf/main.nf -profile docker,your_profile --mtx_annotations /path/to/mtx_annotations --mgx_annotations /path/to/mgx_annotations --outdir /path/to/results
   
   
   

• You can specify multiple profiles separated by comma, e.g. -profile docker,sge.
• Delete the work/ directory after running the pipeline to free up space taken up by intermediate files
• If using awsbatch, you need to specify an S3 bucket as a work directory with the -bucket-dir argument

OR

5. (B): Run the pipeline with only microbeannotator, on protein fasta files. (annotate workflow)

   nextflow run ./meta-microbeannotator-nf/main.nf -profile docker,your_profile -entry annotate --mtx_annotations /path/to/mtx_protein_fastas --mgx_annotations /path/to/mgx_protein_fastas --outdir /path/to/results
   
   
   

Contact

Minghao Chia: [email protected], [email protected]