New module: tobias/bindetect
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- Dominant language
- Nextflow
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- Forks
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- Avg merge
- 1d 6h
- Merged PRs (30d)
- 153
Description
Component
Proposed module: tobias/bindetect.
It wraps TOBIAS BINDetect to estimate transcription factor binding and differential binding from one or more ATAC-seq footprint BigWig tracks, consensus peaks, transcription factor motifs, and a reference FASTA. It emits the complete results directory and global TXT, XLSX, distance, and figure outputs.
This completes a set of three intentionally separate TOBIAS components: ATACorrect, ScoreBigwig, and BINDetect. Their intermediate outputs are independently reusable and can be orchestrated by a TOBIAS footprinting subworkflow.
Software requirements (conda)
channels:
- conda-forge
- bioconda
dependencies:
- bioconda::tobias=0.17.5
Validation
The component has a Docker nf-test stub test and passes nf-core modules lint tobias/bindetect locally (51 checks, no warnings or failures).
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by comparing the existing ATACorrect and ScoreBigwig components, then follow the repository's conventions for the proposed tobias/bindetect module. Use the described TOBIAS 0.17.5 inputs and outputs as the acceptance criteria, and run the Docker nf-test stub plus nf-core modules lint to verify the component is complete.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 68/100