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Fix atlas handling and transform file issues in bundle_seg #267

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Fix atlas handling and transform file issues in bundle_seg

Fix atlas handling and transform file issues in bundle_seg #267

Triggered via pull request December 19, 2024 04:35
@AlexVCaronAlexVCaron
synchronize #80
gagnonanthony:fix/atlasbundleseg
Status Failure
Total duration 1m 42s
Artifacts –

update_pr.yml

on: pull_request
checks  /  compute - changes
17s
checks / compute - changes
checks  /  prettier
15s
checks / prettier
checks  /  editorconfig
16s
checks / editorconfig
checks  /  pre-commit
14s
checks / pre-commit
Matrix: checks / test
Matrix: checks / lint - modules
Matrix: checks / lint - subworkflows
checks  /  report
0s
checks / report
checks  /  status
0s
checks / status
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51 errors and 20 warnings
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-python . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-python" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-java . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-java" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Process returned exit code 127 Launched as "git clone https://github.com/nf-core/setup-nextflow . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-nextflow" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-nextflow/
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-java/
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-python/
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Process completed with exit code 1.
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Process completed with exit code 127.
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Process completed with exit code 127.
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
Process completed with exit code 1.
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-python . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-python" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-java . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-java" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Process returned exit code 127 Launched as "git clone https://github.com/nf-core/setup-nextflow . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-nextflow" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-nextflow/
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-java/
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-python/
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Process completed with exit code 1.
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Process completed with exit code 127.
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Process completed with exit code 127.
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Process completed with exit code 1.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-python . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-python" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-java . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-java" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process returned exit code 127 Launched as "git clone https://github.com/nf-core/setup-nextflow . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-nextflow" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-nextflow/
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-java/
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-python/
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process completed with exit code 127.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process completed with exit code 1.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process completed with exit code 1.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process completed with exit code 127.
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-python . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-python" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-java . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-java" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Process returned exit code 127 Launched as "git clone https://github.com/nf-core/setup-nextflow . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-nextflow" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-nextflow/
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-java/
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-python/
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Process completed with exit code 127.
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Process completed with exit code 127.
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Process completed with exit code 1.
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
Process completed with exit code 1.
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-python . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-python" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Process returned exit code 127 Launched as "git clone https://github.com/actions/setup-java . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-java" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Process returned exit code 127 Launched as "git clone https://github.com/nf-core/setup-nextflow . --config core.autocrlf=false" Launched at "/__w/_actions/Wandalen/setup-nextflow" -> Stderr - sh: 1: git: not found - ' -< Stderr
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-nextflow/
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-java/
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-python/
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Process completed with exit code 127.
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Process completed with exit code 1.
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Process completed with exit code 1.
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Process completed with exit code 127.
checks / status
Process completed with exit code 1.
checks / pre-commit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / prettier
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / editorconfig
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / compute - changes
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
No files were found with the provided path: tests_workdir/. No artifacts will be uploaded.
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
No files were found with the provided path: tests_reports/. No artifacts will be uploaded.
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
No files were found with the provided path: tests_reports/. No artifacts will be uploaded.
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
No files were found with the provided path: tests_workdir/. No artifacts will be uploaded.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
No files were found with the provided path: tests_reports/. No artifacts will be uploaded.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
No files were found with the provided path: tests_workdir/. No artifacts will be uploaded.
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
No files were found with the provided path: tests_reports/. No artifacts will be uploaded.
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
No files were found with the provided path: tests_workdir/. No artifacts will be uploaded.
checks / lint - subworkflows (bundle_seg) / lint - bundle_seg
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - modules (registration/synthregistration) / lint - registration/synthregistration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - modules (registration/anattodwi) / lint - registration/anattodwi
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - subworkflows (registration) / lint - registration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - modules (registration/ants) / lint - registration/ants
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
No files were found with the provided path: tests_reports/. No artifacts will be uploaded.
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
No files were found with the provided path: tests_workdir/. No artifacts will be uploaded.
checks / status
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636