CWL-RNAseq.rst

Running CWL RNAseq

This workflow maps read-pairs to reference genome and produces the transcript

Requirements:

• CWLtool
• Docker

Download this tutorial:

$sudo add-apt-repository universe
$sudo apt update
$sudo apt install subversion

#cloning this tutorial
$svn checkout https://github.com/isb-cgc/RunningWorkflows-on-the-GoogleCloud/trunk/CWL-RNAseq

To install Docker and CWL, you can visit our Cheatsheet listed below:

• Cheatsheet

Starting folder CWL-RNAseq should look like this:

.
└── CWL-RNAseq
    ├── create_bam.cwl
    ├── create_transcript.cwl
    ├── CWL-RNAseq.cwl
    ├── CWL-RNAseq.yml
    ├── data
    │   ├── sample_1.fq
    │   ├── sample_2.fq
    │   ├── sample.fa
    │   └── sample.gtf
    ├── hisat2_align.cwl
    └── index_build.cwl

Let's run it by using:

$cwltool CWL-RNAseq.cwl CWL-RNAseq.yml

If you receive this error: "docker: Got permission denied while trying to connect to the Docker daemon socket at unix"

Try:

$sudo groupadd docker
$sudo usermod -aG docker ${USER}
close and reopen VM then run the script again

After CWLtool finishes:

• CWL-RNAseq.cwl is the main cwl file that connects all other cwl tools together
• CWL-RNAseq.yml is the file that contains all the inputs that are necessary to run the pipeline
• index_build.cwl builds index files from a Fasta file, using Hisat2-build
• hisat2_align.cwl builds a sam file from forward and reverse reads, and the indices built from previous step, using Hisat2
• create_bam.cwl builds a bam file from the newly built sam file, using Samtools
• create_transcript.cwl creates transcript from the bam file from previous step, using Stringtie

Let's take a look at the folder after cwltool finishes:

.
└── CWL-RNAseq
    ├── create_bam.cwl
    ├── create_transcript.cwl
    ├── CWL-RNAseq.cwl
    ├── CWL-RNAseq.yml
    ├── data
    │   ├── sample_1.fq
    │   ├── sample_2.fq
    │   ├── sample.fa
    │   └── sample.gtf
    ├── [final_ref.gtf]
    ├── [final_transcript.gtf]
    ├── [final.tsv]
    ├── hisat2_align.cwl
    ├── [hisat2_align_out]
    │   ├── [hisat2_align_out.log]
    │   └── [sample.sam]
    ├── [hisat2_build.log]
    ├── index_build.cwl
    ├── [sample]
    │   ├── [index.1.ht2]
    │   ├── [index.2.ht2]
    │   ├── [index.3.ht2]
    │   ├── [index.4.ht2]
    │   ├── [index.5.ht2]
    │   ├── [index.6.ht2]
    │   ├── [index.7.ht2]
    │   └── [index.8.ht2]
    └── [sample.bam]