week_4.md

Week 4 (30 May to 6 June)

• Summary
• Working with CWL

Summary

This week starting days is dedicated to the common workflow language which allows for easier design and manipulation of tools in a workflow.CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes.

Working with CWL

I started working with CWL with the help of docs and working on the example which is there in the docs guide and some from CWl-example-repo. Then I started working on simple example like fastq-dump tool which is the intial step of the two-mappers-example.

For running CWL tool for fastq-dumb we have to make two files

• fastq.cwl :- This file contains the workflow. This file will be provided with input and output and some base commands which will help to execute the process. The docker is required in most of the process where this tool is installed or you can install the tool locally on your machine.

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

hints:
  DockerRequirement:
    dockerPull: inutano/sra-toolkit

inputs:
  sraFile:
    type: File
    inputBinding:
      position: 1


baseCommand: [fastq-dump, --split-files, --skip-technical, --gzip]

outputs:
  fastq:
    type: stdout

stdout: $(inputs.out_fastq_prefix).fastq

• A yml file which have the path to the input or it can also have commands etc. So, I've given the path of the sra file for the fastq-dump process to occur.

sraFile:
  class: File
  path: data/ERR045788.sra

out_fastq_prefix: _OUT_FASTQ_PREFIX_

For running cwl tool for gunzip

Then second task is gunzip it

• gnuzip.cwl file :- Which will help to uncompress the gz.

cwlVersion: v1.0

class: CommandLineTool

baseCommand: [gunzip, -c]

inputs:
  gzipfile:
    type: File
    inputBinding:
      position: 1

outputs:
  unzipped_vcf:
    type: stdout

stdout: unzipped.vcf

• A input.yml file for providing the path

infile:
  class: File
  path: data/input.vcf.gz