🎨🍏 Add `autometa --version` to autometa nextflow files #271

evanroyrees · 2022-05-11T16:35:22Z

🐚🐛 Replace incorrect variable name of $coverage with $coverages in bash autometa.sh workflow

Add tracking of autometa version in nextflow processes

The echo "TODO" > autometa.version.txt within the autometa nextflow processes have been replaced with the recently added autometa --version command. This is now being redirected to the retrieved process name as defined by

# ...
def software = getSoftwareName(task.process)
# ...
autometa --version | sed "s/autometa: //g" > ${software}.version.txt

Fix variable name bug in autometa bash workflow

The coverages output is assigned the $coverages variable, but is called $coverage within the autometa-binning entrypoint. This has been updated to the appropriate variable ($coverages) as defined earlier in the script.
The autometa version is now emitted at the beginning of the autometa.sh workflow with autometa --version

PR checklist

This comment contains a description of changes (with reason).
Have you followed the pipeline conventions in the contribution docs

🐚🐛 Replace incorrect variable name of with in bash autometa.sh workflow

github-actions · 2022-05-11T16:39:53Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit a370fa0

+| ✅  62 tests passed       |+
#| ❔  34 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

readme - README did not have a Nextflow minimum version badge.
readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
schema_lint - Schema $id should be https://raw.githubusercontent.com/autometa/master/nextflow_schema.json
Found https://raw.githubusercontent.com/autometa/main/nextflow_schema.json
schema_description - No description provided in schema for parameter: plaintext_email
schema_description - No description provided in schema for parameter: custom_config_version
schema_description - No description provided in schema for parameter: custom_config_base
schema_description - No description provided in schema for parameter: hostnames
schema_description - No description provided in schema for parameter: show_hidden_params
schema_description - No description provided in schema for parameter: singularity_pull_docker_container

❔ Tests ignored:

files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File is ignored: .github/workflows/branch.yml
files_exist - File is ignored: .github/workflows/ci.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: assets/nf-core-autometa_logo_light.png
files_exist - File is ignored: docs/usage.md
files_exist - File is ignored: docs/output.md
files_exist - File is ignored: docs/images/nf-core-autometa_logo.png
files_exist - File is ignored: docs/images/nf-core-autometa_logo_light.png
files_exist - File is ignored: docs/images/nf-core-autometa_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.md
nextflow_config - nextflow_config
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File does not exist: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File does not exist: assets/nf-core-autometa_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-autometa_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-autometa_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: .gitignore or foo
actions_ci - '.github/workflows/ci.yml' not found
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/Autometa/Autometa/.github/workflows/awstest.yml
template_strings - template_strings

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .markdownlint.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yaml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: lib/WorkflowAutometa.groovy
files_exist - File found: modules.json
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .travis.yml
files_unchanged - .gitattributes matches the template
files_unchanged - .markdownlint.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - assets/multiqc_config.yaml matches the template
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: docker_autometa.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: pytest_codecov.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: docker_mock_data_reporter.yml
actions_schema_validation - Workflow validation passed: docker_get_genomes_for_mock.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json

Run details

nf-core/tools version 2.2
Run at 2022-05-11 16:39:33

Sidduppal

Looks good!

🎨🍏 Add autometa --version to nextflow files

a370fa0

🐚🐛 Replace incorrect variable name of with in bash autometa.sh workflow

evanroyrees added bug Something isn't working enhancement New feature or request labels May 11, 2022

evanroyrees self-assigned this May 11, 2022

Sidduppal A50A approved these changes May 11, 2022

View reviewed changes

evanroyrees merged commit d7053cb into dev May 11, 2022

evanroyrees deleted the nxf-autometa-version branch May 11, 2022 16:43

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🎨🍏 Add `autometa --version` to autometa nextflow files #271

🎨🍏 Add `autometa --version` to autometa nextflow files #271

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

🎨🍏 Add autometa --version to autometa nextflow files #271

🎨🍏 Add autometa --version to autometa nextflow files #271

Conversation

Add tracking of autometa version in nextflow processes

Fix variable name bug in autometa bash workflow

PR checklist

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Choose a reason for hiding this comment

🎨🍏 Add `autometa --version` to autometa nextflow files #271

🎨🍏 Add `autometa --version` to autometa nextflow files #271

`nf-core lint` overall result: Passed ✅ ⚠️