nIMP3 workflow

	Developed by the Bork Group in collaboration with the IMP developers Raise an issue or contact us See our other Software & Services	Contributors: Christian Schudoma Mahdi Robbani Daniel Podlesny	Collaborators: Anna Heintz-Buschart Patrick May Oskar Hickl
The development of this workflow was supported by NFDI4Microbiota

---

Description

IMP (Integrated Meta-omic Pipeline) is a workflow for metagenomic/metatranscriptomic co-assembly originally developed at the University of Luxembourg*. nIMP3 is a nextflow-port of IMP3 developed at EMBL Heidelberg in collaboration with the University of Luxembourg and University of Amsterdam for the NFDI4Microbiota framework. nIMP3 is powered by the independent nevermore workflow component library.

Citation

This workflow:

Also cite:

Narayanasamy S, Jarosz Y, Muller EE, et al. IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. Genome Biol. 2016;17(1):260. Published 2016 Dec 16. doi:10.1186/s13059-016-1116-8

---

Overview

---

Requirements

We recommend running nIMP3 with Docker/Singularity. By default, it makes use of the biocontainers versions of its dependencies (with the exception of bwa/samtools, see below)

Essential/Mandatory

• megahit
• bwa
• samtools

NOTE: bwa and samtools need to be run from a shared container/environment.

Optional

• bbmap (bbduk, reformat)
• kraken2
• sortmeRNA
• FastQC
• MultiQC

---

Usage

Cloud-based Workflow Manager (CloWM)

This workflow will be available on the CloWM platform (coming soon).

Command-Line Interface (CLI)

The workflow run is controlled by environment-specific parameters (see run.config) and study-specific parameters (see params.yml). The parameters in the params.yml can be specified on the command line as well.

You can either clone this repository from GitHub and run it as follows

git clone https://github.com/grp-bork/nIMP3.git
nextflow run /path/to/nIMP3 [-resume] -c /path/to/run.config -params-file /path/to/params.yml

Or, you can have nextflow pull it from github and run it from the $HOME/.nextflow directory.

nextflow run grp-bork/nIMP3 [-resume] -c /path/to/run.config -params-file /path/to/params.yml

Input files

Fastq files are supported and can be either uncompressed (but shouldn't be!) or compressed with gzip or bzip2. Sample data must be arranged in one directory per sample.

Per-sample input directories

All files in a sample directory will be associated with the name of the sample folder. Paired-end mate files need to have matching prefixes. Mates 1 and 2 can be specified with suffixes _[12], _R[12], .[12], .R[12]. Lane IDs or other read id modifiers have to precede the mate identifier. Files with names not containing either of those patterns will be assigned to be single-ended. Samples consisting of both single and paired end files are assumed to be paired end with all single end files being orphans (quality control survivors).