Introduction to scientific workflow management systems

Overview

Teaching: 0 min
Exercises: 0 min

Questions

• Key question (FIXME)

Objectives

• First learning objective. (FIXME)

Workflow description

We will assemble a simple workflow easy to understand for anyone who attended basic biology classes. The goal of this workflow is to predict Open Reading Frames (ORFs) from RNA sequences and filter these predicted ORFs to keep only those containing the specific amino acids (sub)sequence “VERA”.

Although very simple, our implemetation will demonstrate:

• how to load remote data into Galaxy
• how to assemble multiple steps into a workflow
• how to use the split-apply-combine strategy

Here is a step-by-step overview:

• Step 1: download a fasta file containing RNA sequence from ensembl
• Step 2: split fasta file in eg 10 files (for parallel processing)
• Step 3: translate the sequence with an ORF finder (here I used a getorf wrapper on emboss)
• Step 4: filter for desired pattern
• Step 5: merge back translated fastq files
• Step 6: extract the original transcript IDs

Key Points

• First key point. Brief Answer to questions. (FIXME)