-# Turning a shell script into a workflow using existing tools
+# Turning a shell script into a workflow by composing existing tools
-In this lesson we will turn `rnaseq_analysis_on_input_file.sh` into a workflow.
+## Introduction
+
+The goal of this training is to walk through the development of a
+best-practices CWL workflow by translating an existing bioinformatics
+shell script into CWL. Specific knowledge of the biology of RNA-seq
+is *not* a prerequisite for these lessons.
+
+These lessons are based on "Introduction to RNA-seq using
+high-performance computing (HPC)" lessons developed by members of the
+teaching team at the Harvard Chan Bioinformatics Core (HBC). The
+original training, which includes additional lectures about the
+biology of RNA-seq can be found here:
+
+https://github.com/hbctraining/Intro-to-rnaseq-hpc-O2
+
+## Background
+
+RNA-seq is the process of sequencing RNA in a biological sample. From
+the sequence reads, we want to measure the relative number of RNA
+molecules appearing in the sample that were produced by particular
+genes. This analysis is called "differential gene expression".
+
+The entire process looks like this:
+
+
+
+For this training, we are only concerned with the middle analytical
+steps (skipping adapter trimming).
+
+* Quality control (FASTQC)
+* Alignment (mapping)
+* Counting reads associated with genes
+
+## Analysis shell script
+
+This analysis is already available as a Unix shell script, which we
+will refer to in order to build the workflow.
+
+Some of the reasons to use CWL over a plain shell script: portability,
+scalability, ability to run on platforms that are not traditional HPC.
+
+rnaseq_analysis_on_input_file.sh
+
+```
+#!/bin/bash
+
+# Based on
+# https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/07_automating_workflow.html
+#
+
+# This script takes a fastq file of RNA-Seq data, runs FastQC and outputs a counts file for it.
+# USAGE: sh rnaseq_analysis_on_input_file.sh <name of fastq file>
+
+set -e
+
+# initialize a variable with an intuitive name to store the name of the input fastq file
+fq=$1
+
+# grab base of filename for naming outputs
+base=`basename $fq .subset.fq`
+echo "Sample name is $base"
+
+# specify the number of cores to use
+cores=4
+
+# directory with genome reference FASTA and index files + name of the gene annotation file
+genome=rnaseq/reference_data
+gtf=rnaseq/reference_data/chr1-hg19_genes.gtf
+
+# make all of the output directories
+# The -p option means mkdir will create the whole path if it
+# does not exist and refrain from complaining if it does exist
+mkdir -p rnaseq/results/fastqc
+mkdir -p rnaseq/results/STAR
+mkdir -p rnaseq/results/counts
+
+# set up output filenames and locations
+fastqc_out=rnaseq/results/fastqc
+align_out=rnaseq/results/STAR/${base}_
+counts_input_bam=rnaseq/results/STAR/${base}_Aligned.sortedByCoord.out.bam
+counts=rnaseq/results/counts/${base}_featurecounts.txt
+
+echo "Processing file $fq"
+
+# Run FastQC and move output to the appropriate folder
+fastqc $fq
+
+# Run STAR
+STAR --runThreadN $cores --genomeDir $genome --readFilesIn $fq --outFileNamePrefix $align_out --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard
+
+# Create BAM index
+samtools index $counts_input_bam
+
+# Count mapped reads
+featureCounts -T $cores -s 2 -a $gtf -o $counts $counts_input_bam
+```
## Setting up
We will create a new git repository and import a library of existing
tool definitions that will help us build our workflow.
-1. Select "Terminal->New terminal"
-
-2. Create a new git repository to hold our workflow with this command:
+Create a new git repository to hold our workflow with this command:
```
git init rnaseq-cwl-training-exercises
git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
```
-3. Go to File->Open Folder and select rnaseq-cwl-training-exercises
-
-4. Go to the terminal window
-
-5. Import bio-cwl-tools with this command:
+Next, import bio-cwl-tools with this command:
```
git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
## Writing the workflow
-### 1.
+### 1. File header
Create a new file "main.cwl"
fastqc:
run: bio-cwl-tools/fastqc/fastqc_2.cwl
in:
- reads_file: fq
+ reads_file: fq
out: [html_file]
```
As of this writing, the `subread` package that provides
`featureCounts` is not available in bio-cwl-tools (and if it has been
added since writing this, let's pretend that it isn't there.) We will
-dive into how to write a CWL wrapper for a command line tool in
-lesson 2. For now, we will leave off the final step.
+go over how to write a CWL wrapper for a command line tool in
+lesson 3. For now, we will leave off the final step.
### 7. Workflow Outputs
projects / rnaseq-cwl-training.git / blobdiff