docs(README.md): update project information

A number of small changes are applied, including an updated project description, corrected repo links, a link out to our WorkflowHub page, and several smaller typos.

README.md

@@ -1,12 +1,12 @@
-# BIC092 - sc/snRNAseq Snakemake Workflow
+# polya_liftover - sc/snRNAseq Snakemake Workflow
 
 [![MIT License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 [![Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-[![CI/CD](https://github.com/IMS-Bio2Core-Facility/BIC092/actions/workflows/cicd.yaml/badge.svg)](https://github.com/IMS-Bio2Core-Facility/BIC092/actions/workflows/cicd.yaml)
+[![CI/CD](https://github.com/IMS-Bio2Core-Facility/polya_liftover/actions/workflows/cicd.yaml/badge.svg)](https://github.com/IMS-Bio2Core-Facility/polya_liftover/actions/workflows/cicd.yaml)
 [![Codestyle: Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Codestyle: snakefmt](https://img.shields.io/badge/code%20style-snakefmt-000000.svg)](https://github.com/snakemake/snakefmt)
 
-A [Snakemake][sm] workflow for using USCS Liftover with Cellranger.
+A [Snakemake][sm] workflow for using PolyA_DB and UCSC Liftover with Cellranger.
 
 Some genes are not accurately annotated in the reference genome.
 Here,
@@ -20,6 +20,10 @@ we can run the whole thing in an isolated environment.
 
 ## Notes on Installation
 
+Ourpipeline is available on Github
+(see below!) and on
+[WorkflowHub][wh].
+
 ### Necessary Software
 
 This pipeline needs [conda][conda]
@@ -51,7 +55,7 @@ It's a bit more challenging for other operating systems.
 Your best bet is to follow their instructions
 [here][sing_install].
 But don't worry!
-**Singularity is _not_ regquired!**
+**Singularity is _not_ required!**
 Snakemake will still run each step in its own Conda environment,
 it just won't put each Conda environment in a container.
 
@@ -62,7 +66,7 @@ page on github and download the most recent version.
 The following will do the trick:
 
 ```shell
-curl -s https://api.github.com/repos/IMS-Bio2Core-Facility/BIC092/releases/latest |
+curl -s https://api.github.com/repos/IMS-Bio2Core-Facility/polya_liftover/releases/latest |
 grep tarball_url |
 cut -d " " -f 4 |
 tr -d '",' |
@@ -83,7 +87,7 @@ for the bleeding edge,
 please clone the repo like so:
 
 ```shell
-git clone https://github.com/IMS-Bio2Core-Facility/BIC092
+git clone https://github.com/IMS-Bio2Core-Facility/polya_liftover
 ```
 
 > :warning: **Heads Up!**
@@ -148,13 +152,21 @@ gene coordinates were updated with [PolyA_DB][polya] version 3,
 converted to more recent builds with [Liftover][liftover],
 and referenced/counted with [Cellranger][cr].
 
+## Future work
+
+- [ ] Improve species and build handling. See [#2][i2]
+- [ ] Directly download and grep the PolyA_DB data. This will aloow users to specify genes only. [#3][i3]
+
 [sm]: https://snakemake.readthedocs.io/en/stable/index.html "Snakemake"
 [polya]: https://exon.apps.wistar.org/polya_db/v3/index.php "PolyA_DB"
 [liftover]: https://genome.ucsc.edu/cgi-bin/hgLiftOver "Liftover"
 [cr]: https://github.com/alexdobin/STAR "Cellranger"
 [conda]: https://docs.conda.io/en/latest/ "Conda"
 [sing]: https://sylabs.io/singularity/ "Singularity"
+[wh]: https://workflowhub.eu/workflows/263 "WorkflowHub"
 [mambaforge]: https://github.com/conda-forge/miniforge#mambaforge "Mambaforge"
 [sing_install]: https://sylabs.io/guides/3.8/admin-guide/installation.html#installation-on-windows-or-mac "Singularity Install"
-[releases]: https://github.com/IMS-Bio2Core-Facility/BIC092/releases "Releases"
+[releases]: https://github.com/IMS-Bio2Core-Facility/polya_liftover/releases "Releases"
 [sm_bp]: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html "Best Practices"
+[i2]: https://github.com/IMS-Bio2Core-Facility/polya_liftover/issues/2 "Issue 2"
+[i3]: https://github.com/IMS-Bio2Core-Facility/polya_liftover/issues/3 "Issue 3"