REDMANE Workflow Team Update

intakes/11-Summer-2024-2025/index.md

@@ -132,17 +132,27 @@ What we learned was the importance of setting up secure and scalable cloud-based
 
 # REDMANE Workflows
 
-The challenge that we were trying to solve was ... ipsum dolor sit amet, consectetur adipiscing elit. Phasellus sit amet turpis lacus. Morbi a risus sed nunc venenatis vehicula sed sit amet tortor. Integer leo metus, scelerisque quis gravida quis, laoreet sed nisl. Duis lacus diam, dapibus id orci nec, pellentesque sollicitudin arcu. Vestibulum auctor nec velit sit amet ornare.
+The challenge that we were trying to convert the raw data files to processed and summarised files.
 
-The way we tried to solve this was ... lorem mauris, ut suscipit dui porta at. Aenean elementum risus vel interdum condimentum. Nunc massa turpis, bibendum in leo vitae, dapibus cursus urna. Integer placerat lacinia finibus. Etiam vitae dolor ut tortor consectetur ultrices eu eget nisi. Cras neque massa, vestibulum id purus nec, aliquam molestie dolor. Vivamus sollicitudin, orci ut bibendum viverra, quam felis viverra purus, ut consectetur diam turpis quis eros.
+The way we tried to solve this was:
 
-What we learned was ... maximus metus id erat pharetra facilisis. Nullam ac urna ultricies diam volutpat faucibus. Sed feugiat placerat est nec scelerisque. Aenean a nisl sit amet ligula gravida fermentum eget in purus. Praesent a dui quis diam bibendum convallis vel in lacus.
+***1. Through Nextflow and Seqera on Milton HPC***
+We learned about the common workflow used in the bioinformatics field, Nextflow, and gained experience with an open-source pipeline designed for variant mapping called nf-core/sarek. This pipeline allowed us to efficiently process WGS data by identifying genetic variants from sequencing datasets. Additionally, we deployed the pipeline on Seqera and executed it on Milton HPC.    
+
+***2. Through Galaxy***
+Galaxy is a user-friendly interface where a lot of bioinformatics tools are available and ready to use.
+
+What we learned include reproducibility and scalability for the two platforms, compared barriers of entry, using both established tools to create workflows and trialing known pipelines. To be able to run Nextflow pipelines using Seqera we explored how to set up the environment on HPC, writing config files, and setting parameters. We've also did the conversion from command line manually using packages like bowtie2, samtools and bcftools. We've also learned how to effectively communicate across teams, sharing files as well as sourcing information about topics we knew less about in daily stand ups and co-working sessions.
+
+We've validated the final output (.vcf files) by visualising it using IGV. 
 
 ## Key links
-- Final presentation slides (if supervisor agrees)
+- [Final Presentation Slides](https://www.canva.com/design/DAGewhgcjlc/-93DtMN5HbugyU98Hr0V4A/edit)
 - Final presentation video (if supervisor agrees)
-- GitHub repos
 - Technical Diary
+  - [Tish's Galaxy Workflow](https://usegalaxy.org.au/u/tishtar/w/basic-conversions)
+  - [GitHub repos](https://github.com/VitaChien/WEHI_Workflow)
+  - [Work Summary](https://wehieduau-my.sharepoint.com/:p:/r/personal/zhao_ch_wehi_edu_au/Documents/Work%20Summary.pptx?d=w3f5a83f7dcb444c0b5e84b955c1282ab&csf=1&web=1&e=oh3yJZ) 
 - Weekly Progress
 - Project Management Tools