Commit c138f0f9 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Merge remote-tracking branch 'nf-core/dev' into dev

parents c79aa4f9 810edea7

README.md

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[![GitHub Actions CI Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/cutandrun/actions?query=workflow%3A%22nf-core+CI%22)

[![GitHub Actions Linting Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/cutandrun/actions?query=workflow%3A%22nf-core+linting%22)

[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/cutandrun/results)

[![DOI](http://img.shields.io/badge/DOI-10.5281/zenodo.5653536-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5653536)

[![DOI](http://img.shields.io/badge/DOI-10.5281/zenodo.5653535-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5653535)



[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)

[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -97,7 +97,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# 


## Citations



If you use  nf-core/cutandrun for your analysis, please cite it using the following doi: [10.5281/zenodo.5653536](https://doi.org/10.5281/zenodo.5653536)

If you use nf-core/cutandrun for your analysis, please cite it using the following doi: [10.5281/zenodo.5653535](https://doi.org/10.5281/zenodo.5653535)



An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

assets/multiqc_config.yaml

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    - fragment_lengths

    - software_versions

    - software_versions_unique



extra_fn_clean_exts:

    - '_val_1'

    - '_val_2'

# Don't show % Dups in the General Stats table (we have this from Picard)

table_columns_visible:

    FastQC:

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