Patch release 1.0.1 #57

itrujnara · 2024-06-14T10:36:33Z

Fixed bugs that caused crashes, removed some unnecessary file publishing

PR checklist

…into bump_version

This reverts commit 8ee48a4.

github-actions · 2024-06-14T10:39:44Z

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

Posted for pipeline commit 23cb132

+| ✅ 215 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗  11 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.1
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
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 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 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
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.

❔ Tests ignored:

files_exist - File is ignored: c
files_exist - File is ignored: o
files_exist - File is ignored: n
files_exist - File is ignored: f
files_exist - File is ignored: /
files_exist - File is ignored: i
files_exist - File is ignored: g
files_exist - File is ignored: e
files_exist - File is ignored: n
files_exist - File is ignored: o
files_exist - File is ignored: m
files_exist - File is ignored: e
files_exist - File is ignored: s
files_exist - File is ignored: .
files_exist - File is ignored: c
files_exist - File is ignored: o
files_exist - File is ignored: n
files_exist - File is ignored: f
files_exist - File is ignored: i
files_exist - File is ignored: g
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ 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-reportho_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-reportho_logo_light.png
files_exist - File found: docs/images/nf-core-reportho_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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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-reportho_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/WorkflowReportho.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
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 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.output_intermediates= false
nextflow_config - Config default value correct: params.use_all= false
nextflow_config - Config default value correct: params.local_databases= false
nextflow_config - Config default value correct: params.offline_run= false
nextflow_config - Config default value correct: params.skip_oma= false
nextflow_config - Config default value correct: params.skip_panther= false
nextflow_config - Config default value correct: params.skip_orthoinspector= false
nextflow_config - Config default value correct: params.orthoinspector_version= Eukaryota2023
nextflow_config - Config default value correct: params.skip_eggnog= false
nextflow_config - Config default value correct: params.use_centroid= false
nextflow_config - Config default value correct: params.min_score= 2.0
nextflow_config - Config default value correct: params.skip_downstream= false
nextflow_config - Config default value correct: params.skip_report= false
nextflow_config - Config default value correct: params.use_structures= false
nextflow_config - Config default value correct: params.iqtree_bootstrap= 1000
nextflow_config - Config default value correct: params.fastme_bootstrap= 100
nextflow_config - Config default value correct: params.skip_orthoplots= false
nextflow_config - Config default value correct: params.skip_iqtree= false
nextflow_config - Config default value correct: params.skip_fastme= false
nextflow_config - Config default value correct: params.skip_treeplots= false
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
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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/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-reportho_logo_light.png matches the template
files_unchanged - docs/images/nf-core-reportho_logo_light.png matches the template
files_unchanged - docs/images/nf-core-reportho_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
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 (180 files)
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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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: awstest.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
multiqc_config - assets/multiqc_config.yml found and not ignored.
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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - IDENTIFY_SEQ_ONLINE found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_OMA_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_PANTHER_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_INSPECTOR_GROUP_ONLINE found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_EGGNOG_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_CSV found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_SCORE_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_HITS found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_ORTHOLOGS found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_HITS_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_HITS found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_STATS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_STATS found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_SEQUENCES_ONLINE found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_AFDB_STRUCTURES found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_TCOFFEETEMPLATE found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - IQTREE found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_IQTREE found in conf/modules.config and Nextflow scripts.
modules_config - CONVERT_PHYLIP found in conf/modules.config and Nextflow scripts.
modules_config - FASTME found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_FASTME found in conf/modules.config and Nextflow scripts.
modules_config - DUMP_PARAMS found in conf/modules.config and Nextflow scripts.
modules_config - CONVERT_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_REPORT 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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-06-14 14:11:40

JoseEspinosa

LGTM, just a small tyop corrected (c/p error likely)

CHANGELOG.md

mashehu · 2024-06-14T11:36:31Z

CHANGELOG.md

+
+### `Fixed`
+
+- Fixed minor bugs that caused compilation errors in the structural alignment section


any way to catch these kind of things with different parameter matrices in the CI tests?

Definitely, I can create a test for that. However, that means quite a lot of extra computation at each CI run. What do you say?

Would be nice if we could move this forward to make available the output of the pipeline into the nf-core web

okay for me if the tests are actually too computationally expensive

JoseEspinosa

Also, seems that test are failing, please fix the issue before merging

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

mashehu · 2024-07-15T11:54:22Z

CHANGELOG.md

+
+### `Fixed`
+
+- Fixed minor bugs that caused compilation errors in the structural alignment section


okay for me if the tests are actually too computationally expensive

JoseEspinosa

The full test have successfully run so I think it is time to release the patch 🎉

itrujnara and others added 9 commits June 11, 2024 14:55

Version bump to 1.1dev

58db340

Merge branch 'nf-core:dev' into bump_version

8a0826d

Merge remote-tracking branch 'upstream/master' into bump_version

c1e5d88

Merge branch 'bump_version' of https://github.com/itrujnara/reportho …

dc27e29

…into bump_version

Fixed bugs in structural alignment

8ee48a4

Revert "Fixed bugs in structural alignment"

facaa98

This reverts commit 8ee48a4.

Fixed bugs in structural alignment

465c75c

Removed unnecessary file publishing

8b10cc8

Version and changelog

13a4dea

JoseEspinosa approved these changes Jun 14, 2024

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CHANGELOG.md Outdated Show resolved Hide resolved

mashehu reviewed Jun 14, 2024

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JoseEspinosa requested changes Jun 14, 2024

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Update CHANGELOG.md

23cb132

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

mashehu approved these changes Jul 15, 2024

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JoseEspinosa approved these changes Jul 18, 2024

View reviewed changes

itrujnara merged commit 42b3051 into nf-core:master Jul 18, 2024


		### `Fixed`

		- Fixed minor bugs that caused compilation errors in the structural alignment section

Patch release 1.0.1 #57

Patch release 1.0.1 #57

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itrujnara commented Jun 14, 2024

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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github-actions bot commented Jun 14, 2024 •

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