Update README.md

README.md

@@ -6,17 +6,17 @@ Marek Kokot, Roozbeh Dehghannasiri, Tavor Baharav, Julia Salzman, and Sebastian
 [SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads](https://www.biorxiv.org/content/10.1101/2023.03.17.533189) 
 bioRxiv (2023)
 
-Kaitlin Chaung, Tavor Baharav,  Ivan Zheludev, Julia Salzman. [SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery
-](https://doi.org/10.1101/2022.06.24.497555), to appear in Cell (2023)
+Kaitlin Chaung, Tavor Baharav, George Henderson, Ivan Zheludev, Peter Wang, Julia Salzman. [SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery
+](https://doi.org/10.1016/j.cell.2023.10.028), Cell (2023)
 
 Tavor Baharav, David Tse, and Julia Salzman. 
 [An Interpretable, Finite Sample Valid Alternative to Pearson’s X2 for Scientific Discovery](https://www.biorxiv.org/content/10.1101/2023.03.16.533008), bioRxiv (2023)
 
 # Introduction
 
-The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
+The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation uses one container per process, making it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 
-# NOMAD
+# SPLASH
 A statistical, reference-free algorithm subsumes myriad problems in genome science and enables novel discovery
 
 ![nomad_1](https://github.com/salzmanlab/nomad/blob/main/assets/nomad_1.png?raw=true "Title")
@@ -26,10 +26,10 @@ A statistical, reference-free algorithm subsumes myriad problems in genome scien
 
 1. Install Java.
 2. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.04.0`).
-3. Depending on your use case, install [`conda`](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html#regular-installation), [`docker`](https://www.docker.com/), or [`singularity`](https://sylabs.io/guides/3.5/user-guide/introduction.html). By using the `docker` or `singularity` nextflow profile, the pipeline can be run within the NOMAD docker container (also available on [dockerhub](https://hub.docker.com/repository/docker/kaitlinchaung/stringstats), which contains all the required dependencies.
+3. Depending on your use case, install [`conda`](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html#regular-installation), [`docker`](https://www.docker.com/), or [`singularity`](https://sylabs.io/guides/3.5/user-guide/introduction.html). By using the `docker` or `singularity` nextflow profile, the pipeline can be run within the SPLASH docker container (also available on [dockerhub](https://hub.docker.com/repository/docker/kaitlinchaung/stringstats), which contains all the required dependencies.
 
 # Try the pipeline
-To test this pipeine, use the command below. The `test` profile will launch a pipeline run with a small dataset.
+To test this pipeline, use the command below. The `test` profile will launch a pipeline run with a small dataset.
 
 How to run with singularity:
 ```bash
@@ -56,14 +56,14 @@ nextflow run salzmanlab/nomad \
 ```
 
 # Usage
-Please see this [document](https://github.com/salzmanlab/nomad/blob/main/docs/usage.md) for descriptions of NOMAD inputs and parameters.
+Please see this [document](https://github.com/salzmanlab/nomad/blob/main/docs/usage.md) for descriptions of SPLASH inputs and parameters.
 # Outputs
-Please see this [document](https://github.com/salzmanlab/nomad/blob/main/docs/output.md) for descriptions of NOMAD output.
+Please see this [document](https://github.com/salzmanlab/nomad/blob/main/docs/output.md) for descriptions of SPLASH output.
 
 
 # Citations
 
-This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) initative, and reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) initiative, and reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
 
 > The nf-core framework for community-curated bioinformatics pipelines.
 >