111 lines
6.6 KiB
Markdown
111 lines
6.6 KiB
Markdown
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<h1>
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<picture>
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<source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-wartanalysis_logo_dark.png">
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<img alt="nf-core/wartanalysis" src="docs/images/nf-core-wartanalysis_logo_light.png">
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</picture>
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</h1>
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[](https://github.com/nf-core/wartanalysis/actions/workflows/ci.yml)
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[](https://github.com/nf-core/wartanalysis/actions/workflows/linting.yml)[](https://nf-co.re/wartanalysis/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
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[](https://www.nf-test.com)
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[](https://www.nextflow.io/)
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[](https://docs.conda.io/en/latest/)
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[](https://www.docker.com/)
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[](https://sylabs.io/docs/)
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[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/wartanalysis)
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[](https://nfcore.slack.com/channels/wartanalysis)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)
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## Introduction
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**nf-core/wartanalysis** is a bioinformatics pipeline that ...
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<!-- TODO nf-core:
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Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
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major pipeline sections and the types of output it produces. You're giving an overview to someone new
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to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
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-->
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<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
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workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->
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<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
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1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
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2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
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## Usage
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> [!NOTE]
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> 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.
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<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
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Explain what rows and columns represent. For instance (please edit as appropriate):
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First, prepare a samplesheet with your input data that looks as follows:
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`samplesheet.csv`:
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```csv
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sample,fastq_1,fastq_2
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CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
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```
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Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
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-->
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Now, you can run the pipeline using:
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<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
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```bash
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nextflow run nf-core/wartanalysis \
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-profile <docker/singularity/.../institute> \
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--input samplesheet.csv \
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--outdir <OUTDIR>
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```
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> [!WARNING]
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> 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**_;
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> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/wartanalysis/usage) and the [parameter documentation](https://nf-co.re/wartanalysis/parameters).
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## Pipeline output
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To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/wartanalysis/results) tab on the nf-core website pipeline page.
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For more details about the output files and reports, please refer to the
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[output documentation](https://nf-co.re/wartanalysis/output).
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## Credits
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nf-core/wartanalysis was originally written by Me.
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We thank the following people for their extensive assistance in the development of this pipeline:
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<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
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## Contributions and Support
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If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
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For further information or help, don't hesitate to get in touch on the [Slack `#wartanalysis` channel](https://nfcore.slack.com/channels/wartanalysis) (you can join with [this invite](https://nf-co.re/join/slack)).
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## Citations
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<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
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<!-- If you use nf-core/wartanalysis for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
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<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
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An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
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You can cite the `nf-core` publication as follows:
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> **The nf-core framework for community-curated bioinformatics pipelines.**
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>
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> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
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>
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> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
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