https://github.com/sanger-tol/curationpretext
A Nextflow DSL2 pipeline for pretext generation in curation
https://github.com/sanger-tol/curationpretext
genomics hic nextflow pipeline
Last synced: 3 months ago
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A Nextflow DSL2 pipeline for pretext generation in curation
- Host: GitHub
- URL: https://github.com/sanger-tol/curationpretext
- Owner: sanger-tol
- License: other
- Created: 2023-07-04T15:03:01.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2026-03-30T14:46:17.000Z (3 months ago)
- Last Synced: 2026-03-30T16:34:43.273Z (3 months ago)
- Topics: genomics, hic, nextflow, pipeline
- Language: Nextflow
- Homepage: https://pipelines.tol.sanger.ac.uk/curationpretext
- Size: 7.06 MB
- Stars: 13
- Watchers: 7
- Forks: 5
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
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README
#  
[](https://github.com/sanger-tol/curationpretext/actions/workflows/nf-test.yml)
[](https://github.com/sanger-tol/curationpretext/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.12773958)
[](https://www.nf-test.com)
[](https://www.nextflow.io/)
[](https://github.com/nf-core/tools/releases/tag/3.5.2)
[](https://docs.conda.io/en/latest/)
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[](https://cloud.seqera.io/launch?pipeline=https://github.com/sanger-tol/curationpretext)
## Introduction
**sanger-tol/curationpretext** is a bioinformatics pipeline typically used in conjunction with [TreeVal](https://github.com/sanger-tol/treeval) to generate pretext maps (and optionally telomeric, gap, coverage, and repeat density plots which can be ingested into pretext) for the manual curation of high quality genomes.
This is intended as a supplementary pipeline for the [treeval](https://github.com/sanger-tol/treeval) project. This pipeline can be simply used to generate pretext maps, information on how to run this pipeline can be found in the [usage documentation](https://pipelines.tol.sanger.ac.uk/curationpretext/usage).
The above image shows the use of this pipeline inside of the manual curation process and follows the below major steps.
1. CRAM_MAP_ILLUMINA_HIC (ALIGN_CRAM) + PAIRS_CREATE_CONTACT_MAPS (CREATE_MAPS) - Generates pretext maps as well as a static image.
2. ACCESSORY_FILES - Generates the repeat density, gap, telomere, and coverage tracks.
3. PRETEXT_INGEST - Imports the generated tracks into pretext for visualisation.
## Usage
> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
Currently, the pipeline uses the following flags:
- `--input`
- The absolute path to the assembled genome in, e.g., `/path/to/assembly.fa`
- `--sample`
- Sample is the naming prefix of the output files, e.g. iyTipFemo
- `--reads`
- The directory of the fasta files generated from longread reads, e.g., `/path/to/fasta/`
- This folder _must_ contain files in a `.fasta.gz` format, or they will be skipped by the internal file search function.
- `--read_type`
- The type of longread data you are utilising, e.g., ont, illumina, hifi.
- `--aligner`
- The aligner you wish to use for the coverage generation, defaults to `AUTO` but options include `bwamem2` and `minimap2`.
- `--cram`
- The directory of the cram _and_ cram.crai files, e.g., `/path/to/cram/`
- `--map_order`
- hic map scaffold order, input either `length` or `unsorted`
- `--teloseq`
- A telomeric sequence, e.g., `TTAGGG`
- `--multi_mapping`
- Level of multi-mapping read filtering to perform whilst building the pretext map.
- `--all_output`
- An option to output all maps + accessory files, the default will only output the pretextmaps where ingestion has occured.
- `--skip_tracks`
- A csv list of accessory tracks to skip, options are: `ALL`, `gap`, `coverage`, `telo`, `repeats`, `NONE`. Default is `NONE`. Please note that capitalization matters.
- `--split_telomere`
- A boolean to also generate the telomere track in 5Prime and 3Prime styles, this is also include the original telomere track.
- `--pre_mapped_bam`
- A boolean option to use `--cram` as input for _A_ pre-mapped bam file.
- `--cram_chunk_size`
- The number of records in a cram file should be chunked into, defaults to 10000.
- `--run_hires`
- A boolean to run the pipeline in hires mode, i.e., generate hires resolution maps. Default is `true`
- `--run_ultra`
- A string argument to run the pipeline in ultra resolution mode, i.e., generate ultra resolution maps. Options are: `yes`, `force`, `no`. Default is `yes`, this runs ultra resolution maps is the genome file is > 4.Gb.
- `--snapshot_order`
- A path to a `genome`, `sizes` or `fai` file containing the scaffolds in the order required for the output snapshot png file.
Now, you can run the pipeline using:
```bash
nextflow run sanger-tol/curationpretext \
--input { input.fasta } \
--cram { path/to/cram/ } \
--reads { path/to/longread/fasta/ } \
--read_type { default is "hifi" }
--sample { default is "pretext_rerun" } \
--teloseq { default is "TTAGGG" } \
--map_order { default is "unsorted" } \
--multi_mapping { default is "0" (for no filtering of multi-mapping reads)} \
--all_output \
--outdir { OUTDIR } \
-profile
```
> **Warning:**
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
For more details, please refer to the [usage documentation](https://pipelines.tol.sanger.ac.uk/curationpretext/usage) and the [parameter documentation](https://pipelines.tol.sanger.ac.uk/curationpretext/parameters).
## Pipeline output
To see the the results of a test run with a full size dataset refer to the [results](https://pipelines.tol.sanger.ac.uk/curationpretext/results) tab on the sanger-tol/curationpretext website pipeline page.
For more details about the output files and reports, please refer to the
[output documentation](https://pipelines.tol.sanger.ac.uk/curationpretext/output).
## Credits
sanger-tol/curationpretext was originally written by Damon-Lee B Pointon (@DLBPointon).
We thank the following people for their extensive assistance in the development of this pipeline:
- @muffato - For reviews.
- @yumisims - TreeVal and Software.
- @weaglesBio - TreeVal and Software.
- @josieparis - Help with better docs and testing.
- @mahesh-panchal - Large support with 1.2.0 in making the pipeline more robust with other HPC environments.
- @GRIT - For feedback and feature requests.
- @prototaxites - Support with 1.3.0 and showing me the power of GAWK.
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
## Citations
If you use sanger-tol/curationpretext for your analysis, please cite it using the following doi: [10.5281/zenodo.12773958](https://doi.org/10.5281/zenodo.12773958)
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).
> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).