Add badges and links to README.md #235

evanroyrees · 2022-02-10T16:41:45Z

No description provided.

🔥 remove requirements.txt 🔥 Remove bioconda recipe meta.yaml 📝 Update docs for nextflow-env.yml ⬆️ Rename environment.yml to nextflow-env.yml ⬆️ Add autometa-env.yml (conda env) to replace requirements.txt (pip requirements file) 🎨 Change Makefile create_environment command to use autometa-env.yml 📝 Change installation directions to correspond to autometa-env.yml rather than requirements.txt

🔥 Reduced build matrix to one os and one python version 📝💚 Added names for downloading test data and running pytest 🐛💚 update conda env explicitly to base (without specifying -n base an 'autometa' env is created

🎨💚 Add tests/environment.yml for pytest/codecov github action

📝 Add full command for building docker image in installation docs

github-actions · 2022-02-10T16:42:54Z

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

Posted for pipeline commit 9b9ea09

+| ✅  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: linting.yml
actions_schema_validation - Workflow validation passed: docker_get_genomes_for_mock.yml
actions_schema_validation - Workflow validation passed: docker_mock_data_reporter.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: docker_autometa.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 2022-02-10 16:42:34

evanroyrees added 17 commits February 9, 2022 15:08

🐛🎨💚🐳 Fix installation method for autometa-env.yml

047efb3

🔥🐛🎨 Remove incorrectly added names

566c700

🎨💚 Add tests/environment.yml for pytest/codecov github action

🐛 fix env being updated

53c3e43

🐛🔥 Remove conda env update target env

a055213

🎨🍏 Re-add names

c7bd8f2

🐛🔥 Remove name where uses was not specified

ad0ebd0

🐛 Add indentation from syntax error

1171293

🐛🎨 Reformat run commands

3546f13

🐛 incorrect path to tests/environment.yml

37bbf2f

🐛 Add target env: -n base

88439fa

⬆️💚 Change trimap install from pip to bioconda

f030582

🐛💚 activate base env b/c installed pkgs are not currently available

c0c553f

📝 Add full command for building docker image in installation docs

🐛 Attempt to fix env update with environ variable -n bioconda-recipes

42f7920

Merge branch 'main' into dev

ee923b8

📝 Add badges and more links to README.md

9b9ea09

evanroyrees merged commit cbbc71b into main Feb 10, 2022

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Add badges and links to README.md #235

Add badges and links to README.md #235

evanroyrees commented Feb 10, 2022

github-actions bot commented Feb 10, 2022

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Add badges and links to README.md #235

Add badges and links to README.md #235

Conversation

evanroyrees commented Feb 10, 2022

github-actions bot commented Feb 10, 2022

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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