Factorize common workflow generation functionality.

[eladrion]

Pull Request Overview

The PR extrapolates functionality for generating CWL and SnakeMake files (e.g. indentation, name generation) into a separate class to reduce code duplication. Also, padding of workflow numbers are now done by using String format tags.

Related Issue

Resolves #137

Changes Introduced

Merely refactoring.

How Has This Been Tested?

Local tests were run on the test suite.

Checklist

• I have referenced a related issue.
• I have followed the project’s style guidelines.
• My changes include tests, if applicable.
• All tests pass locally.
• I have added myself to the CITATION.cff file, if not already present.

[eladrion]

Tested with the following config:
config_refac_137.json
and got as Workflow 3 the following:

# WorkflowNo_2
# This workflow is generated by APE (https://github.com/workflomics/ape).

rule all:
    input:
        'add-path/gProfiler_out_1'

rule XTandem_01:
'    input:
        'add-path/input_1',
        'add-path/input_2'
    output:
        'add-path/XTandem_out_1'
    shell: 'add-path-to-implementation/XTandem {input} {output}'

rule PeptideProphet_02:
'    input:
        'add-path/XTandem_out_1',
        'add-path/input_1',
        'add-path/input_2'
    output:
        'add-path/PeptideProphet_out_1',
        'add-path/PeptideProphet_out_2'
    shell: 'add-path-to-implementation/PeptideProphet {input} {output}'

rule ProteinProphet_03:
'    input:
        'add-path/PeptideProphet_out_1',
        'add-path/input_2'
    output:
        'add-path/ProteinProphet_out_1',
        'add-path/ProteinProphet_out_2'
    shell: 'add-path-to-implementation/ProteinProphet {input} {output}'

rule protXml2IdList_04:
'    input:
        'add-path/ProteinProphet_out_1'
    output:
        'add-path/protXml2IdList_out_1'
    shell: 'add-path-to-implementation/protXml2IdList {input} {output}'

rule gProfiler_05:
'    input:
        'add-path/protXml2IdList_out_1'
    output:
        'add-path/gProfiler_out_1'
    shell: 'add-path-to-implementation/gProfiler {input} {output}'

Does this look good, @CGru21 ?

[eladrion]

This is the respective PNG

[eladrion]

It seems to match the corresponding CWL representation, apart from the placeholder paths:

# WorkflowNo_2
# This workflow is generated by APE (https://github.com/workflomics/ape).
cwlVersion: v1.2
class: Workflow

label: WorkflowNo_2
doc: A workflow including the tool(s) XTandem, PeptideProphet, ProteinProphet, protXml2IdList, gProfiler.

inputs:
  input_1:
    type: File
    format: "http://edamontology.org/format_3244" # mzML
  input_2:
    type: File
    format: "http://edamontology.org/format_1929" # FASTA
steps:
  XTandem_01:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/xtandem/xtandem.cwl
    in:
      XTandem_in_1: input_1
      XTandem_in_2: input_2
    out: [XTandem_out_1]
  PeptideProphet_02:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/peptideprophet/peptideprophet.cwl
    in:
      PeptideProphet_in_1: XTandem_01/XTandem_out_1
      PeptideProphet_in_2: input_1
      PeptideProphet_in_3: input_2
    out: [PeptideProphet_out_1, PeptideProphet_out_2]
  ProteinProphet_03:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/proteinprophet/proteinprophet.cwl
    in:
      ProteinProphet_in_1: PeptideProphet_02/PeptideProphet_out_1
      ProteinProphet_in_2: input_2
    out: [ProteinProphet_out_1, ProteinProphet_out_2]
  protXml2IdList_04:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/protXml2IdList/protXml2IdList.cwl
    in:
      protXml2IdList_in_1: ProteinProphet_03/ProteinProphet_out_1
    out: [protXml2IdList_out_1]
  gProfiler_05:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/gprofiler/gprofiler.cwl
    in:
      gProfiler_in_1: protXml2IdList_04/protXml2IdList_out_1
    out: [gProfiler_out_1]
outputs:
  output_1:
    type: File
    format: "http://edamontology.org/format_3464" # JSON_p
    outputSource: gProfiler_05/gProfiler_out_1

[eladrion]

Hi @vedran-kasalica and @CGru21, I think I am done with this PR which includes some refactorings to make some input handling consistent and otherwise extrapolates common functionality into separate methods to make reuse and extension easier. Also, I added some missing methods for the configuration of the Snakemake export. Please take a look. I will do something else now.

[eladrion]

@CGru21: Waiting with this PR until we have a review on #149 and will afterwards merge. Then I will rebase this branch and ask for reviews.

[CGru21]

I tested this with my snakemake examples and everything looks good.

[eladrion]

Local additional tests also ran successfully

[eladrion]

Merging now