#   [](https://github.com/sanger-tol/curationpretext/actions?query=workflow%3A%22nf-core+CI%22) [](https://github.com/sanger-tol/curationpretext/actions?query=workflow%3A%22nf-core+linting%22)[](https://doi.org/10.5281/zenodo.12773958) [](https://www.nextflow.io/) [](https://www.docker.com/) [](https://sylabs.io/docs/) [](https://tower.nf/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).  1. Generate Maps - Generates pretext maps as well as a static image. 2. Accessory files - Generates the repeat density, gap, telomere, and coverage tracks. ## 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` - `--reads` - The directory of the fasta files generated from longread reads, e.g., `/path/to/fasta/` - `--read_type` - The type of longread data you are utilising, e.g., ont, illumina, hifi. - `--aligner` - The aligner yopu wish to use for the coverage generation, defaults to bwamem2 but minimap2 is also supported. - `--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` - `-entry` - ALL_FILES is the default and generates all accessory files as well as pretext maps - MAPS_ONLY generates only the pretext maps and static images Now, you can run the pipeline using: #### For ALL_FILES run ```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" } \ --outdir { OUTDIR } \ -profile ``` #### For MAPS_ONLY run ```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" } \ --outdir { OUTDIR } \ -profile \ -entry MAPS_ONLY \ ``` > **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. ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#curationpretext` channel](https://nfcore.slack.com/channels/curationpretext) (you can join with [this invite](https://nf-co.re/join/slack)). ## 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. You can cite the `nf-core` publication as follows: > **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).