Dockstore-based workflows with registered tools

Feature Request

Is it possible to create Workflow using Tools registered in Dockstore? I noticed that many available workflows in Dockstore provide all tools (CWL files) locally. I want to write Workflow files (CWL) using tools that I previously registered in Dockstore. Any ideia?

Desired behaviour

A CWL Workflow example:

# ...
steps:
  quality_report:
    run:  registry.hub.docker.com/welliton/rqc # latest version
    in: {}
    out: {}
  quality_control:
    run: registry.hub.docker.com/welliton/trimgalore:v0.4.4 # with tag
    in: {}
    out: {}
# ...

┆Issue is synchronized with this Jira Story ┆fixVersions: Dockstore 2.X ┆friendlyId: DOCK-490 ┆sprint: Backlog ┆taskType: Story

[wdesouza]

Thank you @denis-yuen for your suggestion. It worked! I used the URL for raw Dockstore.cwl file from GithHub. See example below.

cwlVersion: v1.0
class: Workflow

inputs:
  files: File[]
  groups: string[]

outputs:
  qc_report:
    type: File
    outputSource: qc_raw/qc_report

steps:
  qc_raw:
    run: https://raw.githubusercontent.com/labbcb/dockstore-rqc/v3.5/Dockstore.cwl
    in:
      files: files
      groups: groups
    out: [qc_report]

Input example:

files:
  - class: File
    path: ERR127302_1_subset.fastq.gz
  - class: File
    path: ERR127302_2_subset.fastq.gz
groups: [None, None]

I tested using cwltool. Another way is to dowload CWL files via dockstore tool cwl. For example:

dockstore tool cwl --entry registry.hub.docker.com/welliton/rqc:v3.5 > Rqc.cwl

[denis-yuen]

I think that would be nice. There’s a bit of a start of a description of different kinds of imports at https://docs.dockstore.org/en/stable/end-user-topics/language-support.html#converting-file-path-based-imports-to-public-http-s-based-imports-for-wdl and a new section could be added for CWL