NGSManager CLI

⚠️ Work in Progress: This project is under active development. Features may change and improvements are ongoing. Feedback and contributions are welcome!

Command-line tools for running cohesive-ngsmanager pipelines without Jenkins.

Prerequisites

• Linux (tested on AlmaLinux/RHEL)
• Docker installed and running
• Java 11+ (required by Nextflow)
• cohesive-ngsmanager repository cloned locally

Installation

1. Clone this repository

git clone https://github.com/genpat-it/cohesive-ngsmanager-cli.git
cd cohesive-ngsmanager-cli
chmod +x ngsmanager_run.sh

2. Clone cohesive-ngsmanager

git clone https://github.com/genpat-it/cohesive-ngsmanager.git

3. Install Nextflow

curl -s https://get.nextflow.io | bash
mv nextflow ~/.local/bin/
# Or: sudo mv nextflow /usr/local/bin/

# Verify
nextflow -version

Quick Start

# Set the path to ngsmanager (if not in current directory)
export NGSMANAGER_DIR=/path/to/cohesive-ngsmanager

# Run fastp on paired-end files
./ngsmanager_run.sh step_1PP_trimming__fastp.nf reads_R1.fastq.gz reads_R2.fastq.gz

# Results will be in ./ngsmanager_workdir/results/

Usage

./ngsmanager_run.sh <step.nf> <R1.fastq.gz> [R2.fastq.gz] [options...]

Options

Option	Description	Default
--seq_type TYPE	Sequencing type: illumina_paired, ion, nanopore	Auto-detect
--genus_species SP	Species (e.g.: Salmonella_enterica)	-
--cmp CODE	Custom sample code	Auto-generated
--resume	Resume interrupted execution	-

Environment Variables

Variable	Description	Default
NGSMANAGER_DIR	Path to cohesive-ngsmanager	./cohesive-ngsmanager
WORKDIR	Working directory	./ngsmanager_workdir
NEXTFLOW	Path to nextflow	Searches in PATH

Examples

Paired-end Illumina trimming

./ngsmanager_run.sh step_1PP_trimming__fastp.nf sample_R1.fastq.gz sample_R2.fastq.gz

Single-end Ion Torrent

./ngsmanager_run.sh step_1PP_trimming__fastp.nf sample.fastq.gz --seq_type ion

AMR analysis with species

./ngsmanager_run.sh step_4AN_AMR__resfinder.nf R1.fq.gz R2.fq.gz \
    --genus_species Salmonella_enterica

Resume failed execution

./ngsmanager_run.sh step_1PP_trimming__fastp.nf R1.fq.gz R2.fq.gz --resume

Custom working directory

WORKDIR=/data/analysis ./ngsmanager_run.sh step_1PP_trimming__fastp.nf R1.fq.gz R2.fq.gz

Available Steps

Run ./ngsmanager_run.sh without arguments to see all available steps.

Common steps:

Step	Description
step_1PP_trimming__fastp.nf	Quality trimming with fastp
step_1PP_trimming__trimmomatic.nf	Trimming with Trimmomatic
step_2AS_denovo__spades.nf	De novo assembly with SPAdes
step_2AS_denovo__shovill.nf	De novo assembly with Shovill
step_3TX_class__kraken2.nf	Taxonomic classification
step_4AN_AMR__resfinder.nf	AMR detection with ResFinder
step_4AN_AMR__abricate.nf	AMR detection with Abricate
step_4TY_MLST__mlst.nf	MLST typing

Test Step

⚠️ For testing purposes only: test_steps/step_TEST_custom__kmer.nf

This is a test custom step example that demonstrates how to create custom Nextflow steps. It performs k-mer analysis (k=17) using the staphb/seqtk Docker container.

Important: This file is in test_steps/ directory. To use it, you must move it to cohesive-ngsmanager/steps/:

cp test_steps/step_TEST_custom__kmer.nf cohesive-ngsmanager/steps/

Then run it with:

./ngsmanager_run.sh cohesive-ngsmanager/steps/step_TEST_custom__kmer.nf \
  R1.fastq.gz R2.fastq.gz \
  --no-timeout \
  --outdir /mnt/data/results

See test_steps/README.md for more details.

Output Structure

ngsmanager_workdir/
└── results/
    └── {YEAR}/
        └── {CMP}/
            └── {STEP}/
                └── {DS}-{DT}_{METHOD}/
                    ├── result/      # Main outputs (FASTQ, FASTA, etc.)
                    ├── meta/        # Metadata (JSON, log, config)
                    └── qc/          # Quality reports

Troubleshooting

"No space left on device"

The script automatically uses a local .tmp directory (inside WORKDIR) to avoid issues with a full /tmp or root filesystem. It sets:

• NXF_TEMP and TMPDIR to ./ngsmanager_workdir/.tmp
• NXF_HOME to ./ngsmanager_workdir/.nextflow

If you still encounter disk space issues:

1. Use a custom working directory on a partition with more space:

   WORKDIR=/data/myanalysis ./ngsmanager_run.sh step_1PP_trimming__fastp.nf R1.fq.gz R2.fq.gz

2. Clean up previous runs:

   rm -rf ./ngsmanager_workdir/work ./ngsmanager_workdir/.tmp ./ngsmanager_workdir/.nextflow

3. Clean Docker to free up space:

   docker system prune -af

"unexpected file name" or "unexpected RISCD format"

The script handles naming conventions automatically. If you see this error, ensure you're using the latest version of the script.

Pipeline interrupted

Resume with --resume:

./ngsmanager_run.sh step_1PP_trimming__fastp.nf R1.fq.gz R2.fq.gz --resume

License

See cohesive-ngsmanager for license information.