diff --git a/README.md b/README.md index 70e00bc..03ddc64 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ **_An awesome demultiplexing and quality control pipeline_** - [![tests](https://github.com/OpenOmics/weave/workflows/tests/badge.svg)](https://github.com/OpenOmics/weave/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/weave/actions/workflows/doc.yml/badge.svg)](https://github.com/OpenOmics/weave/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/weave?color=brightgreen)](https://github.com/OpenOmics/weave/issues) [![GitHub license](https://img.shields.io/github/license/OpenOmics/weave)](https://github.com/OpenOmics/weave/blob/main/LICENSE) + [![tests](https://github.com/OpenOmics/weave/workflows/tests/badge.svg)](https://github.com/OpenOmics/weave/actions/workflows/dryrun.yaml) [![docs](https://github.com/OpenOmics/weave/actions/workflows/doc.yml/badge.svg)](https://github.com/OpenOmics/weave/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/weave?color=brightgreen)](https://github.com/OpenOmics/weave/issues) [![GitHub license](https://img.shields.io/github/license/OpenOmics/weave)](https://github.com/OpenOmics/weave/blob/main/LICENSE) This is the home of the pipeline, weave. Its long-term goals: to provide accurate quantification, taxonomic classification, and functional profiling of assembled (bacteria and archaea) metagenomes! @@ -18,8 +18,7 @@ The **`./weave`** pipeline is composed of two sub commands to setup and run the > [weave **run**](https://openomics.github.io/weave/usage/run/) > Run the weave pipeline with your input files. - - +> > [weave **cache**](https://openomics.github.io/weave/usage/cache/) > Downloads the reference files for the pipeline to a selected directory. @@ -67,4 +66,4 @@ This site is a living document, created for and by members like you. weave is ma **4.** [Menzel P., Ng K.L., Krogh A. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257](http://www.nature.com/ncomms/2016/160413/ncomms11257/full/ncomms11257.html) **5.** [Wingett SW and Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control [version 2; referees: 4 approved]. F1000Research 2018, 7:1338](https://doi.org/10.12688/f1000research.15931.2) **6.** [Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890.](https://doi.org/10.1093/bioinformatics/bty560) -**7.** [Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019).](https://doi.org/10.1186/s13059-019-1891-0) \ No newline at end of file +**7.** [Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019).](https://doi.org/10.1186/s13059-019-1891-0)