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Solve some Singularity issues. Updates. DSL2 Migration. #57

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Solve some Singularity issues. Updates. DSL2 Migration. #57

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ecdd06b
Migrated to DSL2.
vinjana Mar 6, 2024
5ecc597
Added previous output as reference to the integration test.
vinjana Mar 6, 2024
fed0e20
Typo fix in readme
vinjana Mar 6, 2024
d89566d
Added example output directory.
vinjana Mar 6, 2024
1fc9ae0
Moved process.container config to multiple places, as it was not used…
vinjana Mar 6, 2024
76032e0
Updated Nextflow for the tests. Found a way to combine process option…
vinjana Mar 7, 2024
1c7cef5
Updated Dockerfile and Singularity.def. Moved test/run.sh to integrat…
vinjana Mar 8, 2024
fb45af8
Changed order of integration-test/run.sh parameters.
vinjana Mar 8, 2024
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8 changes: 4 additions & 4 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,15 @@ jobs:
- checkout
- restore_cache:
keys:
- v1-nextflow-env-{{ .Branch }}-{{ checksum "test-environment.yml" }}
- v1-nextflow-env-{{ .Branch }}-{{ checksum "tests-environment.yml" }}
- restore_cache:
keys:
- v1-job-env-{{ .Branch }}-{{ checksum "task-environment.yml" }}
- run:
name: "run integration tests"
command: "test/test1.sh test-results/ mamba nextflowEnv/"
command: "integration-tests/run.sh mamba tests-results/ nextflowEnv/"
- save_cache:
key: v1-nextflow-env-{{ .Branch }}-{{ checksum "test-environment.yml" }}
key: v1-nextflow-env-{{ .Branch }}-{{ checksum "tests-environment.yml" }}
paths:
- nextflowEnv/
- save_cache:
Expand All @@ -38,4 +38,4 @@ jobs:
workflows:
test-workflow:
jobs:
- integration-test
- integration-tests
7 changes: 6 additions & 1 deletion .dockerignore
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Expand Up @@ -9,5 +9,10 @@ work
.circleci
cache
.git
.github
.gitignore
nextflowEnv
*Env/
integration-tests/
.run/
*.log
*Env/
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The addition of *Env/ again at the end of the .dockerignore file seems to be a duplicate entry. This redundancy does not impact the functionality but could be cleaned up for clarity and maintainability.

- *Env/
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

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*Env/

2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -14,3 +14,5 @@ cache/singularity/*
*~
*.sif
.git
.run/
*Env/
53 changes: 0 additions & 53 deletions Dockerfile
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