Resources for Reusing Tools and Scripts

Overview

Teaching: 0 min
Exercises: 0 min

Questions

• How to find other tools/solutions for awkward problems?

Objectives

• tools objectives:

• know good resources for finding solutions to common problems

Learning objectives

By the end of this episode, learners should be aware of where they can look for CWL recipes and more help for common, but awkward, tasks.

Pre-written tool descriptions

When you start a CWL workflow, it is recommended to check if there is already a CWL document available for the tools you want to use. Bio-cwl-tools is a library of CWL documents for biology/life-sciences related tools.

The CWL documents of the previous steps were already provided for you, however, you can also find them in this library. In this episode you will use the bio-cwl-tools library to add the last step to the workflow.

Adding new step in workflow

The last step of our workflow is counting the RNA-seq reads for which we will use the featureCounts tool.

Exercise

Find the featureCounts tool in the bio-cwl-tools library. Have a look at the CWL document. Which inputs does this tool need? And what are the outputs of this tool?

Solution

The featureCounts CWL document can be found at https://github.com/common-workflow-library/bio-cwl-tools/blob/release/subread/featureCounts.cwl ; it has 2 inputs: annotations (line 6) and mapped_reads, both files. These inputs can be found on lines 6 and 9. The output of this tool is a file called featurecounts (line 21).

After finding the featureCounts tool, we need to download the tool to the directory in which our workflow is located. To download the tool, we go to the featureCounts.cwl GitHub page and open the raw file. The screenshot below shows where you can find this button.

There are two approaches to download the CWL document.

1. Copy the script to a new file in an editor, for example VSCode, and save the document in your directory.
2. Use the wget command in the command line. You need to copy the URL of the raw file and use this command:

   wget [URL]
   

Exercise

Use either of the two approaches above to download the featureCounts tool and add the featureCounts tool to the workflow. Similar to the STAR tool, this tool also needs more RAM than the default. To run the tool a minimum of 500 MiB of RAM is needed. Use a requirements entry with ResourceRequirement to allocate a ramMin of 500. Use the inputs and output of the previous exercise to connect this step to previous steps.

Solution

clwVersion: v1.2
class: Workflow

inputs:
  rna_reads_human: File
  ref_genome: Directory
  annotations: File   

steps:
  quality_control:
    run: bio-cwl-tools/fastqc/fastqc_2.cwl
    in:
      reads_file: rna_reads_human
    out: [html_file]

  mapping_reads:
    requirements:
      ResourceRequirement:
        ramMin: 9000
    run: bio-cwl-tools/STAR/STAR-Align.cwl
    in:
      RunThreadN: {default: 4}
      GenomeDir: ref_genome
      ForwardReads: rna_reads_human
      OutSAMtype: {default: BAM}
      SortedByCoordinate: {default: true}
      OutSAMunmapped: {default: Within}
    out: [alignment]

  index_alignment:
    run: bio-cwl-tools/samtools/samtools_index.cwl
    in:
      bam_sorted: mapping_reads/alignment
    out: [bam_sorted_indexed]

  count_reads:
    requirements:
      ResourceRequirement:
        ramMin: 500
    run: bio-cwl-tools/subreads/featureCounts.cwl
    in:
      mapped_reads: index_alignment/bam_sorted_indexed
      annotations: annotations
    out: [featurecounts]

outputs: 
  qc_html:
    type: File
    outputSource: quality_control/html_file
  bam_sorted_indexed:
    type: File
    outputSource: index_alignment/bam_sorted_indexed
  featurecounts:
    type: File
    outputSource: count_reads/featurecounts

The workflow is complete and we only need to complete the YAML input file. The last entry in the input file is the annotations file.

workflow_input.yml

rna_reads_human:
  class: File
  location: rnaseq/raw_fastq/Mov10_oe_1.subset.fq
  format: http://edamontology.org/format_1930
ref_genome:
  class: Directory
  location: rnaseq/hg19-chr1-STAR-index
annotations:
  class: File
  location: rnaseq/reference_data/chr1-hg19_genes.gtf

You have finished the workflow and the input file and now you can run the whole workflow.

cwltool rna_seq_workflow.cwl workflow_input.yml

Key Points

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