nf-core pipeline · archived ·
nf-core/liverctanalysis
A pipeline for quantitative analysis of abdominal CT scans from hepatocellular carcinoma patients.
What nf-core/liverctanalysis is
nf-core/liverctanalysis is a bioinformatics analysis pipeline intended for quantitative examination of abdominal computed tomography (CT) scans taken from patients with hepatocellular carcinoma. The pipeline was originally written by Luis Kuhn Cuellar within the nf-core community framework.
The project was placed under construction during development and has since been archived, meaning it is no longer maintained or updated.
What the pipeline does
The pipeline is implemented in Nextflow DSL2 and structures execution so that individual processes run within dedicated software containers such as Docker or Singularity. Tasks draw from community-curated nf-core modules where available.
Although designed for abdominal CT imaging, the documented processing summary outlines initial read quality checks using FastQC followed by report generation through MultiQC.
Key facts
- Status
- Archived (no longer maintained)
- Original author
- Luis Kuhn Cuellar
- Workflow engine
- Nextflow (version 21.04.0 or higher)
- Target data
- Abdominal CT scans from hepatocellular carcinoma patients
- Supported containers
- Docker, Singularity, Podman, Shifter, Charliecloud
What you can use it for
- Hepatocellular carcinoma CT analysis
- Conducting quantitative analysis on abdominal CT scans obtained from individuals with hepatocellular carcinoma.
- Read quality control
- Evaluating the quality of input sequencing reads using FastQC.
- Quality report aggregation
- Combining quality control results across datasets into a unified presentation using MultiQC.
Strengths and limits
Good at
- Implements Nextflow DSL2 using one container per process for modular dependency isolation.
- Supports multiple container platforms including Docker, Singularity, Podman, Shifter, and Charliecloud for execution consistency.
- Uses standardised process components from nf-core modules.
Watch out for
- The repository is archived and is no longer maintained.
- Development remained under construction, with default listed steps containing placeholder sequencing quality control tools.
- Requires Nextflow version 21.04.0 or later to run.
Questions
Can I run nf-core/liverctanalysis without my own cluster?
The research agent runs nf-core/liverctanalysis with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/liverctanalysis under?
MIT, like every nf-core pipeline.
What is the primary scientific purpose of nf-core/liverctanalysis?
It is intended for quantitative processing and analysis of abdominal CT scans from patients diagnosed with hepatocellular carcinoma.
Is this pipeline actively maintained?
No, the pipeline is archived and not under active maintenance.
What container runtimes are compatible with the pipeline?
It supports Docker, Singularity, Podman, Shifter, and Charliecloud, with Conda available as a fallback.
Who created the pipeline?
It was originally written by Luis Kuhn Cuellar.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/liverctanalysis's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.