Add some details and focus on Software page (#14)

* add Alumni section

* add Alumni section

* add Alumni section

* add poreCov tool

* add Software txt

* add RNAflow tool

* add RIBAP tool

* add VIRify tool

* add new RIBAP img

* fix software images

* add pcago img

* featured tools

* featured tools

* Fix typo (Nextlow -> Nextflow)

---------

Co-authored-by: Matt Huska <[email protected]>

_data/software.yaml

@@ -2,8 +2,11 @@
   group: featured
   image: images/software/breakfast.png
   link: https://github.com/rki-mf1/breakfast
-  description: Fast detection of putative transmission chains in large (>1 million) sets of SARS-CoV-2 genomic sequences
+  description: Fast detection of putative transmission chains in large (>1 million) sets of SARS-CoV-2 genomic sequences.
   repo: rki-mf1/breakfast
+  tags:
+    - Clustering
+    - SARS-CoV-2
 
 # - title: Cool Package
 #   subtitle: a subtitle
@@ -15,14 +18,86 @@
 #   tags:
 #     - resource
 
+- title: poreCoV
+  image: images/software/porecov.jpeg
+  link: https://github.com/replikation/poreCov
+  description: An easy to use, fast, and robust Nextflow pipeline for SARS-CoV-2 genome reconstruction from Nanopore sequencing data. Developed together w/ the [CaSe Group](https://case-group.github.io/).
+  repo: replikation/poreCov
+  tags:
+    - Nextflow
+    - Pipeline
+    - SARS-CoV-2
+
+- title: VIRify
+  image: images/software/virify.png
+  link: https://github.com/EBI-Metagenomics/emg-viral-pipeline
+  description: Detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies. Developed together and mainly maintained by the [Microbiome Informatics](https://www.ebi.ac.uk/about/teams/microbiome-informatics/) team at EBI.
+  repo: EBI-Metagenomics/emg-viral-pipeline
+  tags:
+    - Nextflow
+    - Pipeline
+    - Metagenomics
+    - Viruses
+    - Taxonomy
+
+- title: RNAflow
+  image: images/software/rnaflow.png
+  link: https://github.com/hoelzer-lab/rnaflow
+  description: A portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect differentially expressed genes, aiming for a high level of reproducibility. 
+  repo: hoelzer-lab/rnaflow
+  tags:
+    - Nextflow
+    - Pipeline
+    - RNA-Seq
+    - Gene Expression
+
+- title: RIBAP
+  group: featured
+  image: images/software/ribap.png
+  link: https://github.com/hoelzer-lab/ribap
+  description: A comprehensive bacterial core genome annotation pipeline based on Roary and pairwise Integer Linear Programming. Calculate core genes beyond species levels.
+  repo: hoelzer-lab/ribap
+  tags:
+    - Nextflow
+    - Pipeline
+    - Bacteria
+    - Pangenome
+
 - title: POCP-nf
   image: images/software/pocp-nf.png
   link: https://github.com/hoelzer/pocp
-  description: Nextflow pipeline for the Calculation of the Percentage Of Conserved Proteins following [Qin et al. 2014.](https://www.ncbi.nlm.nih.gov/pubmed/24706738)
+  description: Nextflow pipeline for the Calculation of the **P**ercentage **O**f **C**onserved **P**roteins following [Qin et al. 2014.](https://www.ncbi.nlm.nih.gov/pubmed/24706738) but using DIAMOND instead of BLASTP.
+  repo: hoelzer/pocp
+  tags:
+    - Nextflow
+    - Pipeline
+    - Bacteria
+    - Proteins
+    - Taxonomy
+
+- title: PoSeiDon
+  image: images/software/poseidon.png
+  link: https://github.com/hoelzer/poseidon
+  description: A pipeline for **Po**sitive **Se**lect**i**on **D**etecti**on** and recombination analysis of protein-coding genes.
   repo: hoelzer/pocp
   tags:
-    - nextflow
-    - pipeline
+    - Nextflow
+    - Pipeline
+    - Positive Selection
+    - Recombination
+
+- title: PCAGO
+  image: images/software/pcago.png
+  link: https://github.com/hoelzer-lab/pcago
+  description: Interactive web service that allows analysis of RNA-Seq read count data with PCA and clustering. [Go to web service](https://pcago.bioinf.uni-jena.de/). [Run desktop app](https://github.com/hoelzer-lab/pcago/tree/master/src-electron).
+  repo: hoelzer/pocp
+  tags:
+    - PCA
+    - Clustering
+    - RNA-Seq
+    - Gene expression
+    - Web service
+
 
 # - title: Cool Web App
 #   subtitle: a subtitle

_members/hugues-richard.md

@@ -7,6 +7,8 @@ description: Senior Scientist/PI
 links:
   orcid: 0000-0001-7776-1340
   google-scholar: TzNfNbYAAAAJ
+  twitter: hugues_richard
+  home-page: https://www.lcqb.upmc.fr/hrichard
 ---
 
 Text goes here

software/index.md

@@ -7,8 +7,7 @@ nav:
 
 # {% include icon.html icon="fa-solid fa-wrench" %}Software
 
-Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
-Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+It is important to us that our bioinformatics research also leads to robust, easy-to-use and useful tools for the scientific community. Our tools are available open source and we use workflow management systems like Nextflow and containers like Docker to develop reproducible research software. Have fun trying them out and we're always happy to receive feedback and pull requests on GitHub.   
 
 {% include tags.html tags="publication, resource, website" %}
 

team/index.md

@@ -24,6 +24,8 @@ nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
 
 {% include section.html %}
 
+# {% include icon.html icon="fa-solid fa-users" %}Alumni
+
 {% capture content %}
 
 {% include figure.html image="images/photo.jpg" %}