[FEATURE] CWL/CTD support

[SGSSGene]

Some tests, with raptor and cwl support. All 4 files are validated by cwltool

Raptor build:

./bin/raptor build --export-help cwl

inputs:
  - id: parts
    type: long
    inputBinding:
      prefix: --parts
  - id: kmer
    type: long
    inputBinding:
      prefix: --kmer
  - id: window
    type: long
    inputBinding:
      prefix: --window
  - id: shape
    type: string
    inputBinding:
      prefix: --shape
  - id: output
    type: string
    inputBinding:
      prefix: --output
  - id: size
    type: string
    inputBinding:
      prefix: --size
  - id: hash
    type: long
    inputBinding:
      prefix: --hash
  - id: threads
    type: long
    inputBinding:
      prefix: --threads
  - id: fpr
    type: double
    inputBinding:
      prefix: --fpr
outputs:
  []
id: Raptor
label: Raptor
doc: "Constructs a Raptor index of large collections of nucleotide sequences.\n"
cwlVersion: v1.2
class: CommandLineTool
baseCommand:
  - ./bin/raptor
  - build

Raptor search:

./bin/raptor search --export-help cwl

inputs:
  - id: index
    type: string
    inputBinding:
      prefix: --index
  - id: query
    type: string
    inputBinding:
      prefix: --query
  - id: output
    type: string
    inputBinding:
      prefix: --output
  - id: error
    type: long
    inputBinding:
      prefix: --error
  - id: tau
    type: double
    inputBinding:
      prefix: --tau
  - id: threshold
    type: double
    inputBinding:
      prefix: --threshold
  - id: p_max
    type: double
    inputBinding:
      prefix: --p_max
  - id: fpr
    type: double
    inputBinding:
      prefix: --fpr
  - id: pattern
    type: long
    inputBinding:
      prefix: --pattern
  - id: threads
    type: long
    inputBinding:
      prefix: --threads
outputs:
  []
id: Raptor
label: Raptor
doc: "Searches a Raptor index using one or more sequences queries.\n"
cwlVersion: v1.2
class: CommandLineTool
baseCommand:
  - ./bin/raptor
  - search

Raptor socks (broken/outdated):

./bin/raptor socks --export-help cwl

inputs:
  []
outputs:
  []
id: socks
label: socks
doc: ""
cwlVersion: v1.2
class: CommandLineTool
baseCommand:
  - socks

Raptor upgrade (outdated):

./bin/raptor upgrade --export-help cwl

inputs:
  - id: bins
    type: string
    inputBinding:
      prefix: --bins
  - id: input
    type: string
    inputBinding:
      prefix: --input
  - id: output
    type: string
    inputBinding:
      prefix: --output
  - id: window
    type: boolean
    inputBinding:
      prefix: --window
  - id: kmer
    type: boolean
    inputBinding:
      prefix: --kmer
  - id: parts
    type: boolean
    inputBinding:
      prefix: --parts
outputs:
  []
id: Raptor
label: Raptor
doc: "Upgrades a Raptor index created with an older version of Raptor to be compatible with the currently used version of Raptor.\n"
cwlVersion: v1.2
class: CommandLineTool
baseCommand:
  - ./bin/raptor
  - upgrade

Blocked by:
#193

[vercel]

The latest updates on your projects. Learn more about Vercel for Git ↗︎

Name	Status	Preview	Comments	Updated (UTC)
raptor	✅ Ready (Inspect)	Visit Preview	💬 Add feedback	May 3, 2023 11:26am

[vercel]

@SGSSGene is attempting to deploy a commit to the seqan Team on Vercel.

A member of the Team first needs to authorize it.

[SGSSGene]

Note to myself:
arrays of array in a custom file are bad for cwl. Need a solution.
Here are three ideas:

1. Idea: all inputs as json (via cwl json trick)
2. Idea: escape hatch, by passing sharg, feeding directly into cwl special information.
3. Idea: custom type in sharg and tdl for arrays of array of files

[mr-c]

Thank you @eseiler !