Report #1

nictru · 2024-03-25T14:27:52Z

Add basic report functionality

github-actions · 2024-03-25T14:29:15Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 8b3947a

+| ✅ 182 tests passed       |+
!| ❗  20 tests had warnings |!
-| ❌  53 tests failed       |-

❌ Test failures:

template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L1: {{ tabs(active="conf") }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L11: -{{ key | lower }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L12: -{{ key | lower }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L14: {{ key }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L17: {{ values["description"] }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L31: >{{param}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L35: >{{param}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L37: {{properties["type"]}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L37: {{ " (" + properties["format"] + ")" if "format" in properties }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L40: >{{properties["description"]}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L46: >{{params[param]}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html L48: >{{params["genomes"][params['genome']][param]}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L3: {{ 'active' if active=='tf'}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L6: {{ 'active' if active=='tg'}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L9: {{ 'active' if active=='snp'}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L12: {{ 'active' if active=='conf'}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L17: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L20: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L20: -{{tg}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L20: >{{ tg }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L27: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L29: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L30: {{ pairings | tojson}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L31: {{ tfDiffExp[pairing] }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L40: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L43: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L60: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html L63: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/snp.html L1: {{ tabs(active="snp") }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L1: {{ tabs(active="tf") }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L16: -{{assay}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L16: >{{ assay }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L20: -{{tf}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L22: -{{ tf | lower }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L23: -{{ tf | lower }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L25: {{ tf }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L31: {{color}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L31: {{ color }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L31: {{ assay }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L48: {{ tf_ranking | tojson }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html L49: {{ tf_tg_ranking | tojson }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L1: {{ tabs(active="tg") }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L16: -{{assay}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L16: >{{ assay }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L20: -{{tg}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L22: -{{ tg | lower }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L23: -{{ tg | lower }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L25: {{ tg }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L31: {{color}}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L31: {{ color }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L31: {{ assay }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L48: {{ tg_ranking | tojson }}
template_strings - Found a Jinja template string in /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html L49: {{ tg_tf_ranking | tojson }}

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed

✅ 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: 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/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-tfactivity_logo_light.png
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/images/nf-core-tfactivity_logo_light.png
files_exist - File found: docs/images/nf-core-tfactivity_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: 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: .github/workflows/awsfulltest.yml
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: pipeline_template.yml
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-tfactivity_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: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowTfactivity.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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 with nf-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 manifest.version ends in dev: 1.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.min_peak_occurrence= 1
nextflow_config - Config default value correct: params.window_size= 50000
nextflow_config - Config default value correct: params.decay= true
nextflow_config - Config default value correct: params.expression_aggregation= mean
nextflow_config - Config default value correct: params.affinity_aggregation= max
nextflow_config - Config default value correct: params.min_count= 50
nextflow_config - Config default value correct: params.min_tpm= 1.0
nextflow_config - Config default value correct: params.min_count_tf= 50
nextflow_config - Config default value correct: params.min_tpm_tf= 1.0
nextflow_config - Config default value correct: params.dynamite_ofolds= 3
nextflow_config - Config default value correct: params.dynamite_ifolds= 6
nextflow_config - Config default value correct: params.dynamite_alpha= 0.1
nextflow_config - Config default value correct: params.dynamite_randomize= false
nextflow_config - Config default value correct: params.dynamite_min_regression= 0.1
nextflow_config - Config default value correct: params.alpha= 0.05
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
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 - assets/nf-core-tfactivity_logo_light.png matches the template
files_unchanged - docs/images/nf-core-tfactivity_logo_light.png matches the template
files_unchanged - docs/images/nf-core-tfactivity_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .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: 23.04.0, Config: 23.04.0
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: awstest.yml
actions_schema_validation - Workflow validation passed: fix-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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.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' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
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 2.13.1
Run at 2024-03-25 14:28:58

nictru added 30 commits March 23, 2024 08:25

Init angular project

3a8c756

Implement dummy report creation

4379b6f

Remove dummy code

8b368d5

Prettier

033e8c1

Set up angular material

d015e6d

Switch to jinja

0a2810f

Add basic tf, tg and snp pages

54e66ea

Implement dummy ranking

7a0615c

Add params to file to report

965c006

Improve ranking aggregation

5e965ad

Use real TFs in ranking

bde7da3

Improve style

ca68c5b

Make assays clickable

67feadf

Add first javascript code

db1d897

Implement dynamic ranking

89e562d

Perform initial ranking

c9cb5b6

Make assay traffic light more beautiful

69bb2c1

Improve header style

e63b59c

Add first version of configuration

a161421

Improve configuration visualization

c1ebecf

Add padding for content

3b11cd2

Prettier

37a1df7

Implement TF filter

6cd6e81

Improve handling of unnecessary STARE columns

7eb6452

Prettier

a3f0910

Improve handling of DCG values

68df00a

Improve ranking script

0ac4490

Implement TG DCG calculation

5495d63

Simplify ranking aggregation

4565657

Prepare usage of target genes in report

f93b733

nictru added 19 commits March 24, 2024 21:58

Add visualization of top target genes

e3c00ff

Add g:Profiler integration

9c0a9d7

Make update functions async

1cc2f84

Implement log2fc plots

b216773

Add placeholders for expression plots

d00ce5b

Increase accordion header font size

479f8c0

Convert tfGeneralInfo to macro

b5ffd12

Rename tg_ranking to tf_tg_ranking

64a011f

Add explanation to TF ranking

e30e7b2

Make plots responsive

c71d260

Generalize ranking

2767a90

Outsource ranking logic to separate JS file

ade4eb9

Replicate TF page as TG page

81ccbea

Implement TG ranking

83190b2

Simplify javascript code

258c9ec

Improce ranking logic

78d0d6f

Fix problem with gene ranking

d3c3085

Improve TG view

2d7b214

Update config page

8b3947a

nictru merged commit 22f85a8 into dev Mar 25, 2024
0 of 4 checks passed

nictru deleted the report branch March 25, 2024 14:28

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Report #1

Report #1

nictru commented Mar 25, 2024

github-actions bot commented Mar 25, 2024

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

Report #1

Report #1

Conversation

nictru commented Mar 25, 2024

github-actions bot commented Mar 25, 2024

nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

`nf-core lint` overall result: Failed ❌