sarek
sarek copied to clipboard
Varlociraptor calls
PR checklist
- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
- [ ] If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
- [ ] Make sure your code lints (
nf-core lint
). - [ ] Ensure the test suite passes (
nextflow run . -profile test,docker --outdir <OUTDIR>
). - [ ] Usage Documentation in
docs/usage.md
is updated. - [ ] Output Documentation in
docs/output.md
is updated. - [ ]
CHANGELOG.md
is updated. - [ ]
README.md
is updated (including new tool citations and authors/contributors).
nf-core lint
overall result: Passed :white_check_mark: :warning:
Posted for pipeline commit 097fe18
+| ✅ 140 tests passed |+
#| ❔ 9 tests were ignored |#
!| ❗ 4 tests had warnings |!
:heavy_exclamation_mark: Test warnings:
-
files_exist - File not found:
.github/workflows/awsfulltest.yml
-
nextflow_config - Config
manifest.version
should end indev
:3.3.0
- schema_lint - Input mimetype is missing or empty
-
schema_description - No description provided in schema for parameter:
input_restart
:grey_question: Tests ignored:
-
files_exist - File is ignored:
conf/modules.config
-
files_unchanged - File ignored due to lint config:
assets/nf-core-sarek_logo_light.png
-
files_unchanged - File ignored due to lint config:
docs/images/nf-core-sarek_logo_light.png
-
files_unchanged - File ignored due to lint config:
docs/images/nf-core-sarek_logo_dark.png
-
files_unchanged - File ignored due to lint config:
lib/NfcoreTemplate.groovy
- actions_ci - actions_ci
- template_strings - template_strings
- schema_params - schema_params
- multiqc_config - multiqc_config
:white_check_mark: Tests passed:
-
files_exist - File found:
.gitattributes
-
files_exist - File found:
.gitignore
-
files_exist - File found:
.nf-core.yml
-
files_exist - File found:
.editorconfig
-
files_exist - File found:
.prettierignore
-
files_exist - File found:
.prettierrc.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
orLICENSE.md
orLICENCE
orLICENCE.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/bug_report.yml
-
files_exist - File found:
.github/ISSUE_TEMPLATE/config.yml
-
files_exist - File found:
.github/ISSUE_TEMPLATE/feature_request.yml
-
files_exist - File found:
.github/PULL_REQUEST_TEMPLATE.md
-
files_exist - File found:
.github/workflows/branch.yml
-
files_exist - File found:
.github/workflows/ci.yml
-
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:
assets/nf-core-sarek_logo_light.png
-
files_exist - File found:
conf/test.config
-
files_exist - File found:
conf/test_full.config
-
files_exist - File found:
docs/images/nf-core-sarek_logo_light.png
-
files_exist - File found:
docs/images/nf-core-sarek_logo_dark.png
-
files_exist - File found:
docs/output.md
-
files_exist - File found:
docs/README.md
-
files_exist - File found:
docs/README.md
-
files_exist - File found:
docs/usage.md
-
files_exist - File found:
lib/nfcore_external_java_deps.jar
-
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.yml
-
files_exist - File found:
conf/base.config
-
files_exist - File found:
conf/igenomes.config
-
files_exist - File found:
.github/workflows/awstest.yml
-
files_exist - File found:
lib/WorkflowSarek.groovy
-
files_exist - File found:
modules.json
-
files_exist - File found:
pyproject.toml
-
files_exist - File not found check:
Singularity
-
files_exist - File not found check:
parameters.settings.json
-
files_exist - File not found check:
.nf-core.yaml
-
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:
.github/ISSUE_TEMPLATE/bug_report.md
-
files_exist - File not found check:
.github/ISSUE_TEMPLATE/feature_request.md
-
files_exist - File not found check:
docs/images/nf-core-sarek_logo.png
-
files_exist - File not found check:
.markdownlint.yml
-
files_exist - File not found check:
.yamllint.yml
-
files_exist - File not found check:
lib/Checks.groovy
-
files_exist - File not found check:
lib/Completion.groovy
-
files_exist - File not found check:
lib/Workflow.groovy
-
files_exist - File not found check:
.travis.yml
-
nextflow_config - Config variable found:
manifest.name
-
nextflow_config - Config variable found:
manifest.nextflowVersion
-
nextflow_config - Config variable found:
manifest.description
-
nextflow_config - Config variable found:
manifest.version
-
nextflow_config - Config variable found:
manifest.homePage
-
nextflow_config - Config variable found:
timeline.enabled
-
nextflow_config - Config variable found:
trace.enabled
-
nextflow_config - Config variable found:
report.enabled
-
nextflow_config - Config variable found:
dag.enabled
-
nextflow_config - Config variable found:
process.cpus
-
nextflow_config - Config variable found:
process.memory
-
nextflow_config - Config variable found:
process.time
-
nextflow_config - Config variable found:
params.outdir
-
nextflow_config - Config variable found:
params.input
-
nextflow_config - Config variable found:
params.validationShowHiddenParams
-
nextflow_config - Config variable found:
params.validationSchemaIgnoreParams
-
nextflow_config - Config variable found:
manifest.mainScript
-
nextflow_config - Config variable found:
timeline.file
-
nextflow_config - Config variable found:
trace.file
-
nextflow_config - Config variable found:
report.file
-
nextflow_config - Config variable found:
dag.file
-
nextflow_config - Config variable (correctly) not found:
params.nf_required_version
-
nextflow_config - Config variable (correctly) not found:
params.container
-
nextflow_config - Config variable (correctly) not found:
params.singleEnd
-
nextflow_config - Config variable (correctly) not found:
params.igenomesIgnore
-
nextflow_config - Config variable (correctly) not found:
params.name
-
nextflow_config - Config variable (correctly) not found:
params.enable_conda
-
nextflow_config - Config
timeline.enabled
had correct value:true
-
nextflow_config - Config
report.enabled
had correct value:true
-
nextflow_config - Config
trace.enabled
had correct value:true
-
nextflow_config - Config
dag.enabled
had correct value:true
-
nextflow_config - Config
manifest.name
began withnf-core/
-
nextflow_config - Config variable
manifest.homePage
began with https://github.com/nf-core/ -
nextflow_config - Config
dag.file
ended with.html
-
nextflow_config - Config variable
manifest.nextflowVersion
started with >= or !>= -
nextflow_config - Config
params.custom_config_version
is set tomaster
-
nextflow_config - Config
params.custom_config_base
is set tohttps://raw.githubusercontent.com/nf-core/configs/master
- nextflow_config - Lines for loading custom profiles found
-
files_unchanged -
.gitattributes
matches the template -
files_unchanged -
.prettierrc.yml
matches the template -
files_unchanged -
CODE_OF_CONDUCT.md
matches the template -
files_unchanged -
LICENSE
matches the template -
files_unchanged -
.github/.dockstore.yml
matches the template -
files_unchanged -
.github/CONTRIBUTING.md
matches the template -
files_unchanged -
.github/ISSUE_TEMPLATE/bug_report.yml
matches the template -
files_unchanged -
.github/ISSUE_TEMPLATE/config.yml
matches the template -
files_unchanged -
.github/ISSUE_TEMPLATE/feature_request.yml
matches the template -
files_unchanged -
.github/PULL_REQUEST_TEMPLATE.md
matches the template -
files_unchanged -
.github/workflows/branch.yml
matches the template -
files_unchanged -
.github/workflows/linting_comment.yml
matches the template -
files_unchanged -
.github/workflows/linting.yml
matches the template -
files_unchanged -
assets/email_template.html
matches the template -
files_unchanged -
assets/email_template.txt
matches the template -
files_unchanged -
assets/sendmail_template.txt
matches the template -
files_unchanged -
docs/README.md
matches the template -
files_unchanged -
lib/nfcore_external_java_deps.jar
matches the template -
files_unchanged -
.gitignore
matches the template -
files_unchanged -
.prettierignore
matches the template -
files_unchanged -
pyproject.toml
matches the template - actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
-
readme - README Nextflow minimum version badge matched config. Badge:
23.04.0
, Config:23.04.0
- readme - README Zenodo placeholder was replaced with DOI.
- pipeline_todos - No TODO strings found
- pipeline_name_conventions - Name adheres to nf-core convention
- schema_lint - Schema lint passed
- schema_lint - Schema title + description lint passed
-
system_exit - No
System.exit
calls found - actions_schema_validation - Workflow validation passed: linting.yml
- actions_schema_validation - Workflow validation passed: linting_comment.yml
- actions_schema_validation - Workflow validation passed: clean-up.yml
- actions_schema_validation - Workflow validation passed: awstest.yml
- actions_schema_validation - Workflow validation passed: fix-linting.yml
- actions_schema_validation - Workflow validation passed: ci.yml
- actions_schema_validation - Workflow validation passed: branch.yml
- merge_markers - No merge markers found in pipeline files
-
modules_json - Only installed modules found in
modules.json
- modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
Run details
- nf-core/tools version 2.9
- Run at
2023-09-08 15:41:25
Looking good already well there is still much to be done 😆 I just didn't want gitpod to accidentally delete my changes.