nf-reclaim pipeline

scbirlab/nf-reclaim is a Nextflow pipeline to identify bacterial orthologs and putative spectrum of activity of targets with known inhibitors.

Table of contents

• Processing steps
• Requirements
• Quick start
• Inputs
• Outputs
• Credit
• Issues, problems, suggestions
• Further help

Processing steps

scbirlab/nf-reclaim carries out the following steps:

1. Fetch all high confidence targets with inhibitors from ChEMBL
2. Fetch all protein sequences for targets from UniProt
3. Fetch proteomes of query organisms from UniProt
4. BLAST target protein sequences against query organism proteomes
5. Annotate LOEUF genomic constraint scores for human targets
6. Output inhibitors for targets meeting identity, coverage, and LOEUF cutoffs from ChEMBL

In parallel, the pipeline fetches data to assess LOEUF cutoffs for toxicity:

1. Fetch all inhibitors with cell IC50 or CC50 and target biochemical $K_i$ from ChEMBL
2. Fetch all targets of these inhibitors from ChEMBL
3. Filter down to inhibitors that have target biochemical $K_i$ from ChEMBL
4. Output cell line IC50 paired with target biochemical $K_i$

Requirements

You need Nextflow and either Anaconda, Singularity, or Docker to be installed.

First time using Nextflow?

Crick users

If you're at the Crick or your shared cluster has Nextflow and Singularity already installed, try:

module load Nextflow Singularity

Others

Otherwise, if it's your first time using Nextflow on your system, you can install it using conda:

conda install -c bioconda nextflow

You may need to set the NXF_HOME environment variable. For example,

mkdir -p ~/.nextflow
export NXF_HOME=~/.nextflow

To make this a permanent change, you can do something like the following:

mkdir -p ~/.nextflow
echo "export NXF_HOME=~/.nextflow" >> ~/.bash_profile
source ~/.bash_profile

Quick start

The easiest way to get going is by specifying parameters on the command-line:

nextflow run scbirlab/nf-reclaim \
    --organism_id 243273  \
    --min_identity 0.3 \
    --min_coverage 0.5 \
    --min_pchembl 7.0

Here's what the flags mean:

• --organism_id: The Taxon ID of the organism, whih you can find at NCBI or UniProt
• --min_identity (optional): minimum amino acid identity for orthology
• --min_coverage (optional): minimum coverage for orthology
• --min_pchembl (optional): minimum reported pChEMBL (potency) for inhibitors

Other options are available.

Running with Singularity, Docker, or Conda

scbirlab/nf-reclaim runs on a Singularity container engine by default to ensure software versions are consistent. If you have docker installed, you can run using -with-docker to use it instead, or if you have Conda you can run -with-conda.

Running more than one query in parallel

Make a sample sheet (see below) with columns representing the flags above, and, optionally, a nextflow.config file in the directory where you want the pipeline to run. Then simply run:

nextflow run scbirlab/nf-reclaim

Pipeline versions

If you want to run a particular tagged version of the pipeline, such as v0.0.2, you can do so using

nextflow run scbirlab/nf-reclaim -r v0.0.2

For help, use nextflow run scbirlab/nf-reclaim --help.

The first time you run the pipeline on your system, the software dependencies in environment.yml will be installed. This may take several minutes.

Inputs

Command-line usage

The pipeline can be run with command-line arguments:

nextflow run scbirlab/nf-reclaim --organism_id <taxon ID>

The following parameters are required:

--organism_id       Taxon ID for organism
# or if using sample sheet
--sample_sheet      CSV listing Taxon ID for multiple organisms

The following parameters have default options, and are optional.

• min_identity = 35: minimum amino acid identity for orthology
• min_coverage = 0.7: minimum sequence coverage for orthology
• min_loeuf = 0.515: minimum genomic constraint for human targets
• min_pchembl = 6.0: minimum inhibitor pChEMBL
• gnomad_version = "4.1": which gNOMAD version to use for LOEUF values
• tox_cell_lines = ["HCT116","HEK293T",...,"CHO"]: cell lines to fetch toxicity data
• outputs = "outputs": output directory

Sample sheet

You can run multiple combinations in one command using a sample sheet. The sample sheet is a CSV file with one row per combination of parameters to run.

nextflow run scbirlab/nf-reclaim --sample_sheet path/to/sample-sheet.csv

Sample sheet structure

Here is an example of the sample sheet to find all the mycoplasma orthologous putative inhibitors:

organism_id	proteome_name
243273	"Mycoplasma genitalium"

Further examples are in the test directory of this repository.

Config-file usage (recommended)

For reproducibility, self-documentation, and to save typing, parameters with the same names as the command line flags above can be provided in a nextflow.config file in the working directory. For example:

params {
    organism_id = "243273"
}

Or with a sample sheet:

params {
    sample_sheet = "path/to/sample-sheet.csv"
}

Outputs

Outputs are saved in the output folder defined above.

Issues, problems, suggestions

Add to the issue tracker.

Further help

Here are the pages of the software and databases used by this pipeline.

Databases:

• ChEMBL for inhibitors and targets
• UniProt for protein sequences
• NCBI Genbank for taxonomy

Software:

• diamond to BLAST many-against-many protein sequences.