Improving configs for OpenMS dev and DIANN versions over 1.8.1 #441

ypriverol · 2024-11-17T09:29:29Z

PR checklist

coderabbitai · 2024-11-17T09:29:35Z

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github-actions · 2024-11-17T09:30:57Z

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

Posted for pipeline commit c663c2f

+| ✅ 108 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗  11 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
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 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 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 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 ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/ci.yml
files_exist - File is ignored: .gitignore
nextflow_config - nextflow_config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/quantms/quantms/.github/workflows/awstest.yml
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
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/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-quantms_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: docs/images/nf-core-quantms_logo_light.png
files_exist - File found: docs/images/nf-core-quantms_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_ignored.config
files_exist - File found: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-quantms_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowQuantms.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
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/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/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-quantms_logo_light.png matches the template
files_unchanged - docs/images/nf-core-quantms_logo_light.png matches the template
files_unchanged - docs/images/nf-core-quantms_logo_dark.png 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
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/tsv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
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: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: diann_private.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - NFCORE_QUANTMS found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_QUANTMS found in conf/modules.config and Nextflow scripts.
modules_config - MS2RESCORE found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2024-11-23 17:38:43

conf/dev.config

Dev

Compatible with different formats

# Conflicts: # modules/local/add_sage_feat/main.nf # modules/local/diannconvert/main.nf # modules/local/extract_psm/main.nf # modules/local/extract_sample/main.nf # modules/local/generate_diann_cfg/main.nf # modules/local/ms2rescore/main.nf # modules/local/mzmlstatistics/main.nf # modules/local/preprocess_expdesign.nf # modules/local/samplesheet_check.nf # modules/local/sdrfparsing/main.nf # modules/local/spectrum2features/main.nf

remove big-nodes.config

4085296

ypriverol requested review from jpfeuffer and daichengxin November 17, 2024 09:29

jpfeuffer reviewed Nov 17, 2024

View reviewed changes

conf/dev.config Show resolved Hide resolved

move diann 1.9.1beta to config

db259e8

ypriverol linked an issue Nov 17, 2024 that may be closed by this pull request

Include newest DIA-NN version (1.9.2) #439

Open

ypriverol added 4 commits November 17, 2024 19:29

quantms-utils 0.0.11 -> 0.0.12

78d35e9

remove diann version

d9f9fe2

pride slurm added

6e4ef56

pride slurm added

4b4aff0

ypriverol changed the title ~~Recovering the dev idea for OpenMS nightly builds~~ Improving configs for OpenMS dev and DIANN versions over 1.8.1 Nov 18, 2024

ypriverol added 2 commits November 18, 2024 11:07

diann 1.9.1dev -> 1.9.2

26eb83f

diann 1.9.1dev -> 1.9.2

a814355

ypriverol mentioned this pull request Nov 18, 2024

Support for version 1.9.2 bigbio/quantms-utils#33

Merged

ypriverol requested review from jpfeuffer and timosachsenberg November 18, 2024 11:30

ypriverol and others added 12 commits November 18, 2024 11:43

diann 1.9.1dev -> 1.9.2

a0bad9e

private containers login

2c2380a

private containers login

7ea1f4c

private containers login

4512b41

private containers login

70ce58e

private containers login

2c1829c

private containers login

5d77377

private containers login

a626a2a

add diann_private.yml

c328512

add diann_private.yml

82c6318

add diann_private.yml

3f2dce5

Merge pull request bigbio#46 from bigbio/dev

d50c0f3

Dev

daichengxin and others added 8 commits November 19, 2024 17:11

Merge pull request bigbio#47 from ypriverol/dev

2cdd220

Dev

compatible with different formats

9e0487a

Merge pull request #2 from daichengxin/dev

4c6a8cf

Compatible with different formats

quantms-utils 0.0.12 -> 0.0.13

440a182

quantms-utils 0.0.13 -> 0.0.14

df037e2

quantms-utils 0.0.12 -> 0.0.15

effa1ba

quantms-utils 0.0.14 -> 0.0.15

c663c2f

ypriverol merged commit ddcb0cf into bigbio:dev Nov 23, 2024
21 checks passed

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Improving configs for OpenMS dev and DIANN versions over 1.8.1 #441

Improving configs for OpenMS dev and DIANN versions over 1.8.1 #441

ypriverol commented Nov 17, 2024

coderabbitai bot commented Nov 17, 2024

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Improving configs for OpenMS dev and DIANN versions over 1.8.1 #441

Improving configs for OpenMS dev and DIANN versions over 1.8.1 #441

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ypriverol commented Nov 17, 2024

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coderabbitai bot commented Nov 17, 2024

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

CodeRabbit Configuration File (`.coderabbit.yaml`)

github-actions bot commented Nov 17, 2024 •

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