nf-core pipeline · permafrost
nf-core/troughgraph
Quantitative assessment of permafrost landscapes and regional thaw levels built using Nextflow.
What nf-core/troughgraph is
nf-core/troughgraph is an analysis pipeline designed for the quantitative assessment of permafrost landscapes. By analysing these landscapes, it evaluates the extent of permafrost thaw across a study region.
The pipeline was originally developed by @ftschirpke within the nf-core initiative. It addresses the need for standardised workflows in permafrost monitoring and environmental research.
Permafrost degradation significantly alters landscape morphology and surface stability. Providing structured analytical workflows helps researchers track environmental change and landscape degradation systematically.
What the pipeline does
The pipeline executes automated processing tasks managed through Nextflow. In its documented stages, it incorporates read quality control with FastQC followed by report aggregation using MultiQC.
Key facts
- Pipeline framework
- Nextflow / nf-core
- Original developer
- @ftschirpke
- Domain
- Permafrost landscape assessment
- Quality control tools
- FastQC, MultiQC
What you can use it for
- Permafrost landscape assessment
- Conducting quantitative analysis of permafrost terrain structures to evaluate landscape conditions.
- Permafrost thaw evaluation
- Assessing the level and progression of permafrost thaw across a specified geographic region.
- Sequencing read quality control
- Checking raw input quality using FastQC and compiling summary metrics via MultiQC.
Run it here
The research agent runs nf-core/troughgraph 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.
Strengths and limits
Good at
- Targets specialised quantitative assessment of permafrost terrain and thaw levels.
- Integrated within the community-curated nf-core Nextflow framework.
Watch out for
- Template sections in documentation indicate several configuration and parameter options remain under active development.
- Detailed analytical algorithms beyond quality control steps are not documented in the available release materials.
Questions
Can I run nf-core/troughgraph without my own cluster?
The research agent runs nf-core/troughgraph 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/troughgraph under?
MIT, like every nf-core pipeline.
What is the primary objective of nf-core/troughgraph?
It provides a quantitative assessment of permafrost landscapes to determine regional levels of permafrost thaw.
Who developed nf-core/troughgraph?
The pipeline was originally written by @ftschirpke.
What tools are listed in the pipeline workflow?
The pipeline documents read quality control performed by FastQC and visual report aggregation by MultiQC.
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/troughgraph's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.