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+ - "Marine omics workflow " +contributors: + - Marie59 + +--- + +# Workflow context + +The workflow used as an example here goes from : +- First, produce a protein FASTA file from a nucleotide FASTA file using Prodigal (a tool that predicts protein-coding genes from DNA sequences). +- Then, use InterProscan to create a tabular. Interproscan is a batch tool to query the InterPro database. It helps identify and predict the functions of proteins by comparing them to known databases. +- Finally, discover SanntiS both to build genbank and especially to detect and annotate biosynthetic gene clusters (BGCs). +--- + +## The workflow itself + +![Marine Omics identifying biosynthetic gene clusters worflow image](./images/workflow_marino.png) +--- + +## Run the workflow + +Import and run the following workflow https://earth-system.usegalaxy.eu/u/marie.josse/w/marine-omics-identifying-biosynthetic-gene-clusters + +To know more on how to do that follow the tutorial https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/tutorial.html +--- + + +## Generate the RO-Crate + +Once you run the workflow you can generate the RO-Crate. To do so follow the tutorial https://training.galaxyproject.org/training-material/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html +--- + + +### From workflow to RO-Crate + +![From workflow to RO-Crate](./images/workflow_rocrate.png) +--- + +### The RO-Crate folder and architecture + +![From workflow to RO-Crate](./images/all_tree_structure.png) +--- + +### Let's dive into the ro-crate-metadata.json + +![Date of RO-Crate creation and other informations](./images/rocrate1.png) +--- + +### Description of the RO-Crate structure + +![Description of the RO-Crate structure](./images/rocrate2.png) +--- + +### Galaxy Provenance + +![Date of RO-Crate creation and other informations](./images/rocrate3.png) +--- + +### Title and workflow details + +![Title and details of the workflow](./images/rocrate4.png) +--- + +### Dates + +![Dates of running the workflow and creation of the RO-Crate](./images/rocrate5.png) +--- + +### Data + +![Data uploaded for the workflow and produced by it](./images/rocrate6.png) +--- + +### First tool Prodigal + +![Details on Prodigal](./images/rocrate7.png) +--- + +### Second tool Regex Find and Replace + +![Details on Regex Find and Replace](./images/rocrate8.png) +--- + +### Third tool InterProScan + +![Details on InterProScan](./images/rocrate9.png) +--- + +### Fourth tool SanntiS to build Genbank + +![Details on SanntiS to build Genbank](./images/rocrate10.png) +--- + +### Fourth tool SanntiS to annotate biosynthetic gene clusters + +![Details on SanntiS to annotate biosynthetic gene clusters](./images/rocrate11.png) +--- + +### Details on the different files in the RO-Crate + +![Details on the different files in the RO-Crate](./images/rocrate12.png) +--- + +### End of the ro-crate-metadata.json + +![Details on the different files in the RO-Crate and end of the ro-crate-metadata.json](./images/rocrate13.png) +--- + +### Thank you! + +Try to do the same on your workflow! + + + +