cwl docker

 

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

label: echo
doc: |
  NCBI BlastN Nucleotide-Nucleotide BLAST

requirements:
  InlineJavascriptRequirement: {}
  ResourceRequirement:
    coresMax: 3
    ramMax: 10240


hints:
  DockerRequirement:
    dockerPull: busybox:1.36
  SoftwareRequirement:
    packages:
      blast:
        specs: [ https://bio.tools/blast ]
        version: [ "2.15.0" ]
arguments:
  - valueFrom: $(runtime.cores)
    position: 2

inputs:
  message:
    type: string
    # A default value that can be overridden, e.g. --message "Hola mundo"
    default: "Hello World"
    # Bind this message value as an argument to "echo".
    inputBinding:
      position: 1

outputs: []
baseCommand: ["echo"]

[root@bios cellxgene]# cwltool  --strict-cpu-limit  --strict-memory-limit  cc.cwl
INFO /usr/local/bin/cwltool 3.1.20230719185429
INFO Resolved 'cc.cwl' to 'file:///opt/zcy/cellxgene/cc.cwl'
INFO [job cc.cwl] /tmp/wpft111o$ docker \
    run \
    -i \
    --mount=type=bind,source=/tmp/wpft111o,target=/cBJKeD \
    --mount=type=bind,source=/tmp/j8qmvbwa,target=/tmp \
    --workdir=/cBJKeD \
    --read-only=true \
    --user=0:0 \
    --rm \
    --cidfile=/tmp/xvi2z5wk/20240903113406-036800.cid \
    --env=TMPDIR=/tmp \
    --env=HOME=/cBJKeD \
    --memory=10240m \
    --cpus=3 \
    busybox:1.36 \
    echo \
    'Hello World' \
    3
Hello World 3
INFO [job cc.cwl] Max memory used: 0MiB
INFO [job cc.cwl] completed success
{}INFO Final process status is success