Fix atlas handling and transform file issues in `bundle_seg` #267

Annotations

10 errors and 2 warnings

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

Pre Setup Java

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

Pre Setup nextflow

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

Post Setup nextflow

Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-nextflow/

Post Setup Java

Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-java/

Post Setup Python

Expects action path `action.yml` or `action.yaml` in the action dir: /__w/_actions/Wandalen/setup-python/

Collect test reports

Process completed with exit code 1.

Tests logs

Process completed with exit code 127.

Clean up

Process completed with exit code 127.