Updates to README, usage, output, citations, and references to CMA-->corrmeta awaiting bioconductor release #6

wsjung · 2024-02-13T07:19:27Z

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/multiomicintegration 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).

…tion

synchronizing with nf-core template

… new config file for testing cma + mea modules

…ied to run CMA and MEA

… s3 glob support

….json, and modified samplesheet schema_input.json

…nimal test data

…ry, mea/preprocess, mmap/mmap_parse

… Removed stringr import from mea/go_analysis/templates/ORA_cmd.R as it is not needed and causes namespace dependency issues. updated main workflow

…ich has been renamed CMA-->corrmeta and waiting for bioconductor release

github-actions · 2024-02-13T07:26:46Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 8a0b302

+| ✅ 167 tests passed       |+
!| ❗  18 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

files_exist - File must be removed: lib/nfcore_external_java_deps.jar
files_unchanged - .github/workflows/branch.yml does not match the template
files_unchanged - .github/workflows/linting_comment.yml does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template
files_unchanged - assets/email_template.html does not match the template
files_unchanged - assets/email_template.txt does not match the template
files_unchanged - assets/nf-core-omicsgenetraitassociation_logo_light.png does not match the template
files_unchanged - docs/images/nf-core-omicsgenetraitassociation_logo_light.png does not match the template
files_unchanged - docs/images/nf-core-omicsgenetraitassociation_logo_dark.png does not match the template
files_unchanged - pyproject.toml does not match the template

❗ 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: 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 main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in WorkflowOmicsgenetraitassociation.groovy: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
schema_lint - Input mimetype is missing or empty
schema_description - Ungrouped param in schema: email

✅ 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-omicsgenetraitassociation_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-omicsgenetraitassociation_logo_light.png
files_exist - File found: docs/images/nf-core-omicsgenetraitassociation_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/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: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowOmicsgenetraitassociation.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: 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-omicsgenetraitassociation_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 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.gene_col_name= markname
nextflow_config - Config default value correct: params.pval_col_name= meta_p
nextflow_config - Config default value correct: params.numtests= 17551
nextflow_config - Config default value correct: params.alpha= 0.05
nextflow_config - Config default value correct: params.mmap_header= 1
nextflow_config - Config default value correct: params.mmap_pval_col= p_vals
nextflow_config - Config default value correct: params.mmap_beta_col= betas_genes
nextflow_config - Config default value correct: params.mmap_se_genes= se_genes
nextflow_config - Config default value correct: params.pascal_header= 0
nextflow_config - Config default value correct: params.pascal_pval_col= 1
nextflow_config - Config default value correct: params.outdir= results
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.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 - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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
template_strings - Did not find any Jinja template strings (111 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 2.12.1
Run at 2024-02-13 07:26:28

wsjung and others added 29 commits January 21, 2024 20:59

updated nextflow.config with pipeline rename to omicsgenetraitassocia…

932f56b

…tion

Template update for nf-core/tools version 2.11.1

ac5cc35

Merge branch 'TEMPLATE' into dev

43c9225

synchronizing with nf-core template

added modules CMA, MMAP, and PASCAL

38fbb0d

fixed versions emit values for cma/main.nf and pascal/main.nf

e7a673b

added when directives to cma/main.nf

cc9b742

added MEA modules

4de0c29

pipeline works from CMA to MEA

6886178

added config for CMA and MEA configs in modules.config

966b810

updated .gitignore to exclude downloaded singularity images and added…

53e00b3

… new config file for testing cma + mea modules

added temporary subworkflow CMA_SUBWORKFLOW which will later be modif…

ddd9790

…ied to run CMA and MEA

commented out workflow initialization and validation steps for testing

7be6ed2

pascal/main.nf edited to extract tarball as nextflow does not support…

1e422f7

… s3 glob support

fixed versions emit name

f582449

added test_local.config, modules.config, and updated subworkflows

4287b6e

Merge branch 'dev' into dev

657b278

added pipeline parameters to nextflow.config, updated nextflow_schema…

00dbcb7

….json, and modified samplesheet schema_input.json

deleted --genome required input check from initialise

e1f3869

added module configs to modules.config and edited test.config with mi…

fb76480

…nimal test data

added biocontainers for cma/format_cma_input, mea/merge_ora_and_summa…

200cf09

…ry, mea/preprocess, mmap/mmap_parse

added meta map propagation or TODOs to do so

a9c7bb5

updated subworkflows to match updated modules

7c0308a

updated main workflow with updated subworkflows

b529c8c

Merge branch 'dev' of github.com:wsjung/MultiomicIntegration into dev

4ccd46e

added TODO notes for modules that have been requested a biocontainer.…

98d6061

… Removed stringr import from mea/go_analysis/templates/ORA_cmd.R as it is not needed and causes namespace dependency issues. updated main workflow

Merge branch 'dev' into dev

fa9a91c

updated output.md and CITATIONS.md

1502bb6

updated usage.md and added samplesheet.csv to assets

8f3d0f7

updated README with metro map. updated container for cma R package wh…

8a0b302

…ich has been renamed CMA-->corrmeta and waiting for bioconductor release

wsjung added 2 commits February 13, 2024 11:01

fixed nf-core lint test failures

64b33a0

updated files to match editorconfig linting

4171993

wsjung closed this Feb 13, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Updates to README, usage, output, citations, and references to CMA-->corrmeta awaiting bioconductor release #6

Updates to README, usage, output, citations, and references to CMA-->corrmeta awaiting bioconductor release #6

wsjung commented Feb 13, 2024 •

edited

Loading

github-actions bot commented Feb 13, 2024 •

edited

Loading

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

Updates to README, usage, output, citations, and references to CMA-->corrmeta awaiting bioconductor release #6

Updates to README, usage, output, citations, and references to CMA-->corrmeta awaiting bioconductor release #6

Conversation

wsjung commented Feb 13, 2024 • edited Loading

PR checklist

github-actions bot commented Feb 13, 2024 • edited Loading

nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

wsjung commented Feb 13, 2024 •

edited

Loading

github-actions bot commented Feb 13, 2024 •

edited

Loading

`nf-core lint` overall result: Failed ❌