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Merged
merged 5 commits into from
Oct 6, 2021
Merged

Fewer containers #129

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1d1e387
run the tests against cwltool
mr-c Oct 6, 2021
60e3ded
tests: use only one Python container
mr-c Oct 6, 2021
7098f79
tests: consilidate to a single Debian container
mr-c Oct 6, 2021
c0d787d
tests: specify registry for remaining containers without it
mr-c Oct 6, 2021
a335d19
run CI on 1.2.1 proposed as well
mr-c Oct 6, 2021
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4 changes: 2 additions & 2 deletions .github/workflows/ci.yml
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Expand Up @@ -6,9 +6,9 @@ name: CI
on:
# Triggers the workflow on push or pull request events but only for the main branch
push:
branches: [ main ]
branches: [ main, 1.2.1_proposed ]
pull_request:
branches: [ main ]
branches: [ main, 1.2.1_proposed ]

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
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29 changes: 29 additions & 0 deletions .github/workflows/cwltool.yml
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@@ -0,0 +1,29 @@
name: test_with_cwltool

# Controls when the action will run.
on:
# Triggers the workflow on push or pull request events but only for the main branch
push:
branches: [ main, 1.2.1_proposed ]
pull_request:
branches: [ main, 1.2.1_proposed ]

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:

jobs:
test_with_cwltool:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v2

- uses: actions/setup-python@v2
with:
python-version: '3.9.x'
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@kinow kinow Oct 6, 2021

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I guess cwltool itself needs to be tested with multiple Python versions, but for this repository just 3.9.x line is OK.


- name: Setup prerequirements
run: pip install cwltest cwltool

- name: Run tests against the reference runner
run: ./run_test.sh RUNNER=cwltool EXTRA=--parallel -j$(nproc)
2 changes: 1 addition & 1 deletion tests/binding-test.cwl
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Expand Up @@ -4,7 +4,7 @@ class: CommandLineTool
cwlVersion: v1.2
hints:
- class: DockerRequirement
dockerPull: python:2-slim
dockerPull: docker.io/python:3-slim
inputs:
- id: reference
type: File
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2 changes: 1 addition & 1 deletion tests/bool-empty-inputbinding.cwl
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Expand Up @@ -3,7 +3,7 @@ class: CommandLineTool
cwlVersion: v1.2
hints:
- class: DockerRequirement
dockerPull: python:2-slim
dockerPull: docker.io/python:3-slim
inputs:
- id: flag
type: boolean
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2 changes: 1 addition & 1 deletion tests/bwa-mem-tool.cwl
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Expand Up @@ -8,7 +8,7 @@ hints:
- class: ResourceRequirement
coresMin: 2
- class: DockerRequirement
dockerPull: python:2-slim
dockerPull: docker.io/python:3-slim

inputs:
- id: reference
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2 changes: 1 addition & 1 deletion tests/cat-tool-shortcut.cwl
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Expand Up @@ -5,7 +5,7 @@ cwlVersion: v1.2

requirements:
- class: DockerRequirement
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim

inputs:
file1: stdin
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2 changes: 1 addition & 1 deletion tests/cat3-tool-docker.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2
doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
requirements:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1:
type: File
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2 changes: 1 addition & 1 deletion tests/cat3-tool-mediumcut.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2
doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
requirements:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1:
type: File
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2 changes: 1 addition & 1 deletion tests/cat3-tool-shortcut.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2
doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
requirements:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1:
type: File
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2 changes: 1 addition & 1 deletion tests/cat3-tool.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2
doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1:
type: File
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2 changes: 1 addition & 1 deletion tests/cat4-tool.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2
doc: "Print the contents of a file to stdout using 'cat' running in a docker container if docker is available."
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1: File
outputs:
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2 changes: 1 addition & 1 deletion tests/cat5-tool.cwl
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Expand Up @@ -6,7 +6,7 @@ class: CommandLineTool
doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
hints:
DockerRequirement:
dockerPull: "debian:stretch-slim"
dockerPull: docker.io/debian:stable-slim
ex:BlibberBlubberFakeRequirement:
fakeField: fraggleFroogle
inputs:
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2 changes: 1 addition & 1 deletion tests/dir2.cwl
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Expand Up @@ -4,7 +4,7 @@ requirements:
ShellCommandRequirement: {}
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
indir: Directory
outputs:
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2 changes: 1 addition & 1 deletion tests/docker-array-secondaryfiles.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2

requirements:
- class: DockerRequirement
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
- class: InlineJavascriptRequirement
- class: ShellCommandRequirement

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2 changes: 1 addition & 1 deletion tests/docker-output-dir.cwl
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Expand Up @@ -2,7 +2,7 @@ class: CommandLineTool
cwlVersion: v1.2
requirements:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
dockerOutputDirectory: /other
inputs: []
outputs:
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2 changes: 1 addition & 1 deletion tests/docker-run-cmd.cwl
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Expand Up @@ -2,7 +2,7 @@ class: CommandLineTool
cwlVersion: v1.2
requirements:
DockerRequirement:
dockerPull: bash:4.4.12
dockerPull: docker.io/bash:4.4
inputs: []
outputs:
cow:
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2 changes: 1 addition & 1 deletion tests/empty-array-input.cwl
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Expand Up @@ -5,7 +5,7 @@ class: CommandLineTool

hints:
- class: DockerRequirement
dockerPull: python:2-slim
dockerPull: docker.io/python:3-slim

inputs:
- id: array
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2 changes: 1 addition & 1 deletion tests/envvar2.cwl
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Expand Up @@ -6,7 +6,7 @@ requirements:
ShellCommandRequirement: {}
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
arguments: [
echo, {valueFrom: '"HOME=$HOME"', shellQuote: false}, {valueFrom: '"TMPDIR=$TMPDIR"', shellQuote: false},
{valueFrom: '&&', shellQuote: false},
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2 changes: 1 addition & 1 deletion tests/envvar3.cwl
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Expand Up @@ -10,7 +10,7 @@ requirements:
ShellCommandRequirement: {}
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
arguments:
- shellQuote: false
valueFrom: |
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2 changes: 1 addition & 1 deletion tests/formattest2.cwl
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Expand Up @@ -7,7 +7,7 @@ cwlVersion: v1.2
doc: "Reverse each line using the `rev` command"
hints:
DockerRequirement:
dockerPull: "debian:stretch-slim"
dockerPull: docker.io/debian:stable-slim

inputs:
input:
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2 changes: 1 addition & 1 deletion tests/formattest3.cwl
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Expand Up @@ -9,7 +9,7 @@ cwlVersion: v1.2
doc: "Reverse each line using the `rev` command"
hints:
DockerRequirement:
dockerPull: "debian:stretch-slim"
dockerPull: docker.io/debian:stable-slim

inputs:
input:
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2 changes: 1 addition & 1 deletion tests/glob-path-error.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2

requirements:
- class: DockerRequirement
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim

class: CommandLineTool

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2 changes: 1 addition & 1 deletion tests/initialworkdirrequirement-docker-out.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2

requirements:
- class: DockerRequirement
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
- class: InitialWorkDirRequirement
listing:
- $(inputs.INPUT)
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2 changes: 1 addition & 1 deletion tests/inline-js.cwl
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Expand Up @@ -5,7 +5,7 @@ requirements:
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
dockerPull: python:2-slim
dockerPull: docker.io/python:3-slim

inputs:
- id: args.py
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2 changes: 1 addition & 1 deletion tests/iwd/iwd-container-entryname1.cwl
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Expand Up @@ -12,7 +12,7 @@ outputs:
glob: head.txt
requirements:
DockerRequirement:
dockerPull: "debian:10"
dockerPull: docker.io/debian:stable-slim
dockerOutputDirectory: /output
InitialWorkDirRequirement:
listing:
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2 changes: 1 addition & 1 deletion tests/iwd/iwd-container-entryname3.cwl
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Expand Up @@ -12,7 +12,7 @@ outputs:
glob: head.txt
hints:
DockerRequirement:
dockerPull: "debian:10"
dockerPull: docker.io/debian:stable-slim
dockerOutputDirectory: /output
requirements:
InitialWorkDirRequirement:
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2 changes: 1 addition & 1 deletion tests/iwd/iwd-passthrough2.cwl
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Expand Up @@ -9,7 +9,7 @@ doc: |

requirements:
DockerRequirement:
dockerPull: "python:3-slim"
dockerPull: docker.io/python:3-slim
InitialWorkDirRequirement:
listing:
- entryname: "renamed-filelist.txt"
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2 changes: 1 addition & 1 deletion tests/iwd/iwdr_dir_literal_real_file.cwl
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Expand Up @@ -3,7 +3,7 @@ cwlVersion: v1.2

requirements:
DockerRequirement:
dockerPull: debian:stable-slim
dockerPull: docker.io/debian:stable-slim
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
listing: |
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2 changes: 1 addition & 1 deletion tests/loadContents/cwloutput-nolimit.cwl
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Expand Up @@ -3,7 +3,7 @@ class: CommandLineTool
cwlVersion: v1.2
requirements:
DockerRequirement:
dockerPull: "python:3-slim"
dockerPull: docker.io/python:3-slim
inputs:
script:
type: File
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2 changes: 1 addition & 1 deletion tests/metadata.cwl
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Expand Up @@ -18,7 +18,7 @@ dct:creator:

hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1:
type: File
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2 changes: 1 addition & 1 deletion tests/networkaccess.cwl
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Expand Up @@ -2,7 +2,7 @@ class: CommandLineTool
cwlVersion: v1.2
requirements:
DockerRequirement:
dockerPull: python:3
dockerPull: docker.io/python:3-slim
NetworkAccess:
networkAccess: true
inputs: []
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2 changes: 1 addition & 1 deletion tests/networkaccess2.cwl
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Expand Up @@ -2,7 +2,7 @@ class: CommandLineTool
cwlVersion: v1.2
requirements:
DockerRequirement:
dockerPull: python:3
dockerPull: docker.io/python:3-slim
inputs: []
outputs: []
baseCommand: python
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2 changes: 1 addition & 1 deletion tests/no-inputs-tool.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2
doc: "CommandLineTool without inputs."
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs: []
outputs:
output:
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2 changes: 1 addition & 1 deletion tests/no-inputs-wf.cwl
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Expand Up @@ -17,7 +17,7 @@ steps:
doc: "CommandLineTool without inputs."
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs: []
outputs:
output:
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2 changes: 1 addition & 1 deletion tests/no-outputs-tool.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: v1.2
doc: "CommandLineTool without outputs."
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1:
type: File
Expand Down
2 changes: 1 addition & 1 deletion tests/no-outputs-wf.cwl
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Expand Up @@ -15,7 +15,7 @@ steps:
doc: "CommandLineTool without outputs."
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1:
type: File
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2 changes: 1 addition & 1 deletion tests/optional-output.cwl
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Expand Up @@ -4,7 +4,7 @@ cwlVersion: "v1.2"
doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
hints:
DockerRequirement:
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim
inputs:
file1:
type: File
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2 changes: 1 addition & 1 deletion tests/revsort.cwl
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Expand Up @@ -10,7 +10,7 @@ cwlVersion: v1.2
# in which the command line tools will execute.
hints:
- class: DockerRequirement
dockerPull: debian:stretch-slim
dockerPull: docker.io/debian:stable-slim


# The inputs array defines the structure of the input object that describes
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4 changes: 2 additions & 2 deletions tests/search.cwl
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Expand Up @@ -14,7 +14,7 @@ $graph:
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
dockerPull: python:2-slim
dockerPull: docker.io/python:3-slim

inputs:
file: File
Expand Down Expand Up @@ -48,7 +48,7 @@ $graph:
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
dockerPull: python:2-slim
dockerPull: docker.io/python:3-slim
inputs:
file:
type: File
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2 changes: 1 addition & 1 deletion tests/stage-unprovided-file.cwl
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Expand Up @@ -2,7 +2,7 @@ cwlVersion: v1.2
class: CommandLineTool
hints:
- class: DockerRequirement
dockerPull: python:2-slim
dockerPull: docker.io/python:3-slim
inputs:
- id: infile
type: File?
Expand Down
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