diff --git a/docs/lint_errors.md b/docs/lint_errors.md index c9264460e4..7139c8b3a2 100644 --- a/docs/lint_errors.md +++ b/docs/lint_errors.md @@ -100,7 +100,7 @@ The following variables are depreciated and fail the test if they are still pres * The old method for specifying the pipeline version. Replaced by `manifest.version` * `params.nf_required_version` * The old method for specifying the minimum Nextflow version. Replaced by `manifest.nextflowVersion` -* `process.container` +* `params.container` * The old method for specifying the dockerhub container address. Replaced by `process.container` ## Error #5 - Continuous Integration configuration ## {#5} @@ -110,7 +110,7 @@ This test fails if the following happens: * `.travis.yml` does not contain the string `nf-core lint ${TRAVIS_BUILD_DIR}` under `script` * `.travis.yml` does not contain the string `docker pull :dev` under `before_install` - * Where `` is fetched from `params.container` in the `nextflow.config` file, without the docker tag _(if we have the tag the tests fail when making a release)_ + * Where `` is fetched from `process.container` in the `nextflow.config` file, without the docker tag _(if we have the tag the tests fail when making a release)_ * `.travis.yml` does not test the Nextflow version specified in the pipeline as `manifest.nextflowVersion` * This is expected in the `env` section of the config, eg: @@ -154,7 +154,7 @@ The `README.md` files for a project are very important and must meet some requir > This test only runs when `--release` is set or `$TRAVIS_BRANCH` is equal to `master` -These tests look at `params.container`, `process.container` and `$TRAVIS_TAG`, only +These tests look at `process.container` and `$TRAVIS_TAG`, only if they are set. * Container name must have a tag specified (eg. `nfcore/pipeline:version`) diff --git a/tests/test_lint.py b/tests/test_lint.py index 667b214b82..c179547019 100644 --- a/tests/test_lint.py +++ b/tests/test_lint.py @@ -38,7 +38,7 @@ def pf(wd, path): pf(WD, 'lint_examples/license_incomplete_example')] # The maximum sum of passed tests currently possible -MAX_PASS_CHECKS = 57 +MAX_PASS_CHECKS = 59 # The additional tests passed for releases ADD_PASS_RELEASE = 1 @@ -201,7 +201,7 @@ def test_version_consistency_pass(self): """Tests the workflow version and container version sucessfully""" lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) lint_obj.config["manifest.version"] = "0.4" - lint_obj.config["params.container"] = "nfcore/tools:0.4" + lint_obj.config["process.container"] = "nfcore/tools:0.4" lint_obj.check_version_consistency() expectations = {"failed": 0, "warned": 0, "passed": 1} self.assess_lint_status(lint_obj, **expectations) @@ -213,7 +213,7 @@ def test_version_consistency_with_env_fail(self): os.environ["TRAVIS_REPO_SLUG"] = "nf-core/testpipeline" lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) lint_obj.config["manifest.version"] = "0.4" - lint_obj.config["params.container"] = "nfcore/tools:0.4" + lint_obj.config["process.container"] = "nfcore/tools:0.4" lint_obj.config["process.container"] = "nfcore/tools:0.4" lint_obj.check_version_consistency() expectations = {"failed": 1, "warned": 0, "passed": 0} @@ -226,7 +226,7 @@ def test_version_consistency_with_numeric_fail(self): os.environ["TRAVIS_REPO_SLUG"] = "nf-core/testpipeline" lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) lint_obj.config["manifest.version"] = "0.4" - lint_obj.config["params.container"] = "nfcore/tools:0.4" + lint_obj.config["process.container"] = "nfcore/tools:0.4" lint_obj.check_version_consistency() expectations = {"failed": 1, "warned": 0, "passed": 0} self.assess_lint_status(lint_obj, **expectations) @@ -238,7 +238,7 @@ def test_version_consistency_with_no_docker_version_fail(self): os.environ["TRAVIS_REPO_SLUG"] = "nf-core/testpipeline" lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) lint_obj.config["manifest.version"] = "0.4" - lint_obj.config["params.container"] = "nfcore/tools" + lint_obj.config["process.container"] = "nfcore/tools" lint_obj.check_version_consistency() expectations = {"failed": 1, "warned": 0, "passed": 0} self.assess_lint_status(lint_obj, **expectations) @@ -250,7 +250,7 @@ def test_version_consistency_with_env_pass(self): os.environ["TRAVIS_REPO_SLUG"] = "nf-core/testpipeline" lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) lint_obj.config["manifest.version"] = "0.4" - lint_obj.config["params.container"] = "nfcore/tools:0.4" + lint_obj.config["process.container"] = "nfcore/tools:0.4" lint_obj.check_version_consistency() expectations = {"failed": 0, "warned": 0, "passed": 1} self.assess_lint_status(lint_obj, **expectations)