sarek
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Enable multiple ploidy values for controlfreec
Close #808
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:
Posted for pipeline commit 08d314b
+| ✅ 153 tests passed |+
#| ❔ 9 tests were ignored |#
:grey_question: Tests ignored:
-
files_exist - File is ignored:
conf/modules.config
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files_exist - File is ignored:
conf/test.config
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files_exist - File is ignored:
conf/test_full.config
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files_unchanged - File ignored due to lint config:
assets/nf-core-sarek_logo_light.png
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files_unchanged - File ignored due to lint config:
docs/images/nf-core-sarek_logo_light.png
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files_unchanged - File ignored due to lint config:
docs/images/nf-core-sarek_logo_dark.png
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files_unchanged - File ignored due to lint config:
lib/NfcoreSchema.groovy
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files_unchanged - File ignored due to lint config:
lib/NfcoreTemplate.groovy
- template_strings - template_strings
:white_check_mark: Tests passed:
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files_exist - File found:
.gitattributes
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files_exist - File found:
.gitignore
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files_exist - File found:
.nf-core.yml
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files_exist - File found:
.editorconfig
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files_exist - File found:
.prettierignore
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files_exist - File found:
.prettierrc.yml
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files_exist - File found:
CHANGELOG.md
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files_exist - File found:
CITATIONS.md
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files_exist - File found:
CODE_OF_CONDUCT.md
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files_exist - File found:
CODE_OF_CONDUCT.md
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files_exist - File found:
LICENSE
orLICENSE.md
orLICENCE
orLICENCE.md
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files_exist - File found:
nextflow_schema.json
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files_exist - File found:
nextflow.config
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files_exist - File found:
README.md
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files_exist - File found:
.github/.dockstore.yml
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.github/CONTRIBUTING.md
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.github/ISSUE_TEMPLATE/bug_report.yml
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.github/ISSUE_TEMPLATE/config.yml
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files_exist - File found:
.github/ISSUE_TEMPLATE/feature_request.yml
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.github/PULL_REQUEST_TEMPLATE.md
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files_exist - File found:
.github/workflows/branch.yml
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.github/workflows/ci.yml
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.github/workflows/linting_comment.yml
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files_exist - File found:
.github/workflows/linting.yml
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files_exist - File found:
assets/email_template.html
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files_exist - File found:
assets/email_template.txt
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files_exist - File found:
assets/sendmail_template.txt
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files_exist - File found:
assets/nf-core-sarek_logo_light.png
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files_exist - File found:
docs/images/nf-core-sarek_logo_light.png
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files_exist - File found:
docs/images/nf-core-sarek_logo_dark.png
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files_exist - File found:
docs/output.md
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files_exist - File found:
docs/README.md
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files_exist - File found:
docs/README.md
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files_exist - File found:
docs/usage.md
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files_exist - File found:
lib/nfcore_external_java_deps.jar
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files_exist - File found:
lib/NfcoreSchema.groovy
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files_exist - File found:
lib/NfcoreTemplate.groovy
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files_exist - File found:
lib/Utils.groovy
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files_exist - File found:
lib/WorkflowMain.groovy
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files_exist - File found:
main.nf
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files_exist - File found:
assets/multiqc_config.yml
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files_exist - File found:
conf/base.config
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files_exist - File found:
conf/igenomes.config
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files_exist - File found:
.github/workflows/awstest.yml
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files_exist - File found:
.github/workflows/awsfulltest.yml
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files_exist - File found:
lib/WorkflowSarek.groovy
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files_exist - File found:
modules.json
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files_exist - File found:
pyproject.toml
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files_exist - File not found check:
Singularity
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files_exist - File not found check:
parameters.settings.json
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files_exist - File not found check:
.nf-core.yaml
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files_exist - File not found check:
bin/markdown_to_html.r
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files_exist - File not found check:
conf/aws.config
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files_exist - File not found check:
.github/workflows/push_dockerhub.yml
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files_exist - File not found check:
.github/ISSUE_TEMPLATE/bug_report.md
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files_exist - File not found check:
.github/ISSUE_TEMPLATE/feature_request.md
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files_exist - File not found check:
docs/images/nf-core-sarek_logo.png
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files_exist - File not found check:
.markdownlint.yml
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files_exist - File not found check:
.yamllint.yml
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files_exist - File not found check:
lib/Checks.groovy
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lib/Completion.groovy
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lib/Workflow.groovy
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files_exist - File not found check:
.travis.yml
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nextflow_config - Config variable found:
manifest.name
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nextflow_config - Config variable found:
manifest.nextflowVersion
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nextflow_config - Config variable found:
manifest.description
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nextflow_config - Config variable found:
manifest.version
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nextflow_config - Config variable found:
manifest.homePage
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timeline.enabled
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trace.enabled
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report.enabled
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dag.enabled
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nextflow_config - Config variable found:
process.cpus
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nextflow_config - Config variable found:
process.memory
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nextflow_config - Config variable found:
process.time
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nextflow_config - Config variable found:
params.outdir
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nextflow_config - Config variable found:
params.input
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nextflow_config - Config variable found:
params.show_hidden_params
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nextflow_config - Config variable found:
params.schema_ignore_params
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nextflow_config - Config variable found:
manifest.mainScript
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nextflow_config - Config variable found:
timeline.file
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nextflow_config - Config variable found:
trace.file
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nextflow_config - Config variable found:
report.file
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nextflow_config - Config variable found:
dag.file
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nextflow_config - Config variable (correctly) not found:
params.nf_required_version
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nextflow_config - Config variable (correctly) not found:
params.container
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nextflow_config - Config variable (correctly) not found:
params.singleEnd
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nextflow_config - Config variable (correctly) not found:
params.igenomesIgnore
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nextflow_config - Config variable (correctly) not found:
params.name
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nextflow_config - Config variable (correctly) not found:
params.enable_conda
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nextflow_config - Config
timeline.enabled
had correct value:true
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nextflow_config - Config
report.enabled
had correct value:true
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nextflow_config - Config
trace.enabled
had correct value:true
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nextflow_config - Config
dag.enabled
had correct value:true
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nextflow_config - Config
manifest.name
began withnf-core/
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nextflow_config - Config variable
manifest.homePage
began with https://github.com/nf-core/ -
nextflow_config - Config
dag.file
ended with.html
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nextflow_config - Config variable
manifest.nextflowVersion
started with >= or !>= -
nextflow_config - Config
manifest.version
ends indev
:'3.2dev'
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nextflow_config - Config
params.custom_config_version
is set tomaster
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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
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files_unchanged -
.gitattributes
matches the template -
files_unchanged -
.prettierrc.yml
matches the template -
files_unchanged -
CODE_OF_CONDUCT.md
matches the template -
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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 -
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.github/workflows/branch.yml
matches the template -
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.github/workflows/linting_comment.yml
matches the template -
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matches the template -
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assets/email_template.html
matches the template -
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assets/email_template.txt
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assets/sendmail_template.txt
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docs/README.md
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lib/nfcore_external_java_deps.jar
matches the template -
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.gitignore
matches the template -
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.prettierignore
matches the template -
files_unchanged -
pyproject.toml
matches the template - actions_ci - '.github/workflows/ci.yml' is triggered on expected events
- actions_ci - '.github/workflows/ci.yml' checks minimum NF version
- actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
-
actions_awsfulltest -
.github/workflows/awsfulltest.yml
is triggered correctly -
actions_awsfulltest -
.github/workflows/awsfulltest.yml
does not use-profile test
-
readme - README Nextflow minimum version badge matched config. Badge:
22.10.1
, Config:22.10.1
- 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
- schema_lint - Input mimetype lint passed: 'text/csv'
- schema_params - Schema matched params returned from nextflow config
-
system_exit - No
System.exit
calls found - actions_schema_validation - Workflow validation passed: clean-up.yml
- actions_schema_validation - Workflow validation passed: linting_comment.yml
- actions_schema_validation - Workflow validation passed: ci.yml
- actions_schema_validation - Workflow validation passed: awstest.yml
- actions_schema_validation - Workflow validation passed: awsfulltest_germline.yml
- actions_schema_validation - Workflow validation passed: linting.yml
- actions_schema_validation - Workflow validation passed: fix-linting.yml
- actions_schema_validation - Workflow validation passed: pytest-workflow.yml
- actions_schema_validation - Workflow validation passed: awsfulltest.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
- multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
- multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
- multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
- modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
Run details
- nf-core/tools version 2.8
- Run at
2023-05-29 10:50:58
Read the docs: https://github.com/BoevaLab/FREEC/blob/271bef4777119e69ae6eaf1e68051e12fae5e529/scripts/makeGraph2.0.R#L5 I think we don't need to supply the ploidy
@nf-core-bot fix linting
The docs lied to me and need to pass an int into the script afterall..... so reverting to previous changes but will also require a module update so turning this back into draft state for the moment
back to this one: first step: bumping the control freec version, so we can use the new makeGraph script and hopefully solve some issues