Sub-workflows

Overview

Teaching: 20 min
Exercises: 0 min

Questions

• How do I reuse a workflow as part of a larger workflow?

• How do I run only a part of a workflow?

Objectives

• Understand how to create a sub-workflow.

• Understand how to run part of a workflow.

Sub-workflows

We have seen previously the Nextflow allows for the definition of reusable processes (modules). Nextflow also allows to define reusable sub-workflows.

Workflow definition

The workflow keyword allows the definition of workflow components that enclose the invocation of one or more processes and operators.

For example:

nextflow.enable.dsl=2

include {QUANT;INDEX} from './modules/module.nf'

workflow RNASEQ_QUANT_PIPE {
  read_pairs_ch = channel.fromFilePairs('data/yeast/reads/*_{1,2}.fq.gz')
  transcriptome_ch = channel.fromPath('data/yeast/transcriptome/*.fa.gz')
  QUANT(INDEX(transcriptome_ch), read_pairs_ch)
}

The above snippet defines a workflow component, named RNASEQ_QUANT_PIPE, that can be invoked from another workflow component definition in the same way as any other function or process i.e. RNASEQ_QUANT_PIPE().

nextflow.enable.dsl=2

include {QUANT;INDEX} from './modules/module.nf'

workflow RNASEQ_QUANT_PIPE {
  read_pairs_ch = channel.fromFilePairs('data/yeast/reads/*_{1,2}.fq.gz')
  transcriptome_ch = channel.fromPath('/data/yeast/transcriptome/*.fa.gz')
  QUANT(INDEX(transcriptome_ch),read_pairs_ch)
}

// Implicit workflow
workflow  {
  /*
  * Call sub-workflow using <WORKFLOWNAME>() syntax
  */
  RNASEQ_QUANT_PIPE()
}

Implicit workflow

A workflow definition which does not declare any name is assumed to be the main workflow, and it is implicitly executed. Therefore it’s the entry point of the workflow application.

Workflow parameters

A workflow component can access any variable and parameter defined in the outer scope.

For example:

nextflow.enable.dsl=2

include {QUANT;INDEX} from './modules/module.nf'

params.transcriptome = '/some/data/file'
read_pairs_ch = channel.fromFilePairs('data/yeast/reads/*_{1,2}.fq.gz')

workflow RNASEQ_QUANT_PIPE {

  transcriptome_ch = channel.fromPath(params.transcriptome)
  QUANT(INDEX(transcriptome_ch),read_pairs_ch)
}

Workflow inputs

A workflow component can declare one or more input channels using the take keyword.

For example:

nextflow.enable.dsl=2

include {QUANT;INDEX} from './modules/rnaseq-tasks.nf'

read_pairs_ch = channel.fromFilePairs('data/yeast/reads/*_{1,2}.fq.gz')
transcriptome_ch = channel.fromPath('data/yeast/transcriptome/*.fa.gz')

workflow RNASEQ_QUANT_PIPE {
    take:
      transcriptome_ch
      read_pairs_ch

    main:
      INDEX(transcriptome_ch)
      QUANT(INDEX.out,read_pairs_ch)
}

Warning

When the take keyword is used, the beginning of the workflow body needs to be identified with the main keyword. Then, the input can be specified as an argument in the workflow invocation statement:

These input channels can then be passed to the workflow as parameters inside the (). Multiple parameters are separated by a comma , and must be specified in the order they appear under take:

nextflow.enable.dsl=2

read_pairs_ch = channel.fromFilePairs('data/yeast/reads/*_{1,2}.fq.gz')
transcriptome_ch = channel.fromPath('data/yeast/transcriptome/*.fa.gz')

workflow RNASEQ_QUANT_PIPE {
    take:
      transcriptome_ch
      read_pairs_ch

    main:
      INDEX(transcriptome_ch)
      QUANT(INDEX.out,read_pairs_ch)
}

workflow {
    RNASEQ_QUANT_PIPE(transcriptome_ch,read_pairs_ch)
}

Note

Workflow inputs are by definition channel data structures. If a basic data type is provided instead, ie. number, string, list, etc. it’s implicitly converted to a channel value (i. e. non-consumable).

Workflow outputs

A workflow component can declare one or more output channels using the emit keyword.

For example:

nextflow.enable.dsl=2

include {QUANT;INDEX} from './modules/module.nf'

params.transcriptome = '/some/data/file'
read_pairs_ch = channel.fromFilePairs('data/yeast/reads/*_{1,2}.fq.gz')

workflow RNASEQ_QUANT_PIPE {
    take:
     transcriptome_ch
     read_pairs_ch

    emit:
      QUANT.out

    main:
      INDEX(transcriptome_ch)
      QUANT(INDEX.out,read_pairs_ch)
}

The above script declares one output, QUANT.out.

The result of the RNASEQ_QUANT_PIPE execution can be accessed using the out property i. e. RNASEQ_QUANT_PIPE.out.

When there are multiple output channels declared, use the array bracket notation to access each output component as described for the Process outputs definition.

RNASEQ_QUANT_PIPE.out[0]
RNASEQ_QUANT_PIPE.out[1]

Alternatively, the output channel can be accessed using a name which it’s assigned to in the emit declaration:

For example:

nextflow.enable.dsl=2

workflow RNASEQ_QUANT_PIPE {
   main:
     INDEX(transcriptome_ch)
     QUANT(INDEX.out,read_pairs_ch)

   emit:
     read_quant = QUANT.out
}

The output QUANT.out is assigned the name read_quant The the result of the above snippet can accessed using:

RNASEQ_QUANT_PIPE.out.read_quant

Note

Implicit workflow definition is ignored when a script is included as module. This allows the writing a workflow script that can be used either as a library module or as an application script.

Workflow composition

As with modules workflows components can be defined within your script or imported by a include statment. After which they can be invoked and composed as any other workflow component or process in your script.

nextflow.enable.dsl=2

// file ./modules/qc.nf
include {FASTQC} from './modules.nf'

workflow READ_QC_PIPE {
    take:
      read_pairs_ch
      quant_out_ch

    main:
        FASTQC(read_pairs_ch)

    emit:
        FASTQC.out
}

nextflow.enable.dsl=2

include { READ_QC_PIPE } from './modules/qc.nf'
include { QUANT; INDEX } from './modules/module.nf'
include { MULTIQC } from './modules/multiqc.nf'

workflow RNASEQ_QUANT_PIPE {
    take:
      transcriptome_ch
      read_pairs_ch

    main:
        INDEX(transcriptome)
        QUANT(INDEX.out)

    emit:
        QUANT.out
}

params.transcriptome = '/some/data/file'
read_pairs_ch = channel.fromFilePairs('data/yeast/reads/*_{1,2}.fq.gz')
transcriptome_ch = channel.fromPath(params.transcriptome)

workflow {
    take:
      transcriptome_ch
      read_pairs_ch

    main:
      RNASEQ_QUANT_PIPE(transcriptome_ch, read_pairs_ch)
      READ_QC_PIPE(read_pairs_ch, RNASEQ_QUANT_PIPE.out)
      MULTIQC(RNASEQ_QUANT_PIPE.out.mix(READ_QC_PIPE).collect())
}

Nested workflow execution

Nested workflow execution determines an implicit scope. Therefore the same process can be invoked in two different workflow scopes, like for example in the above snippet INDEX could be used either in RNASEQ_QUANT and RNASEQ_QC. The workflow execution path along with the process names defines the process fully qualified name that is used to distinguish the two different process invocations i.e. RNASEQ_QUANT:INDEX and RNASEQ_QC:INDEX in the above example.

Specific workflow entry points

By default, the unnamed workflow is assumed to be the main entry point for the script. Using named workflows, the entry point can be customised by using the entry option of the run command. This allows users to run a specific sub-workflow or a section of their entire workflow script.

For example:

$ nextflow run main.nf -entry RNASEQ_QUANT_PIPE

The above command would run the RNASEQ_QUANT_PIPE sub-workflow.

Key Points

• Nextflow allows to define reusable sub-workflows.

• Sub-workflow allows the definition of workflow processes that can be included from any other script and invoked as a custom function within the new workflow scope. This enables reuse of workflow components

• The entry option of the nextflow run command specifies the workflow name to be executed