Release candidate for 0.6.0 #129

GallVp · 2024-12-15T23:05:45Z

PR checklist

Correct indents and whitespaces

removed end of line "/"

params.add_attrs_to_proteins_fasta to params.add_attrs_to_gffread_fastas

Rename params.add_attrs_to_proteins_fasta to params.add_attrs_to_gffread_fastas

Add gffread EXTRACT_CDNA and EXTRACT_CDS feature to outputs

… coding genes

Fixed TSEBRA failure issue

Fixed issues in genepal-report

…r length

…es_by_aa_length Added parameter filter_genes_by_aa_length

github-actions · 2024-12-15T23:07:27Z

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

Posted for pipeline commit d069633

+| ✅ 105 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: assets/nf-core-genepal_logo_light.png
files_exist - File is ignored: docs/images/nf-core-genepal_logo_light.png
files_exist - File is ignored: docs/images/nf-core-genepal_logo_dark.png
nextflow_config - nextflow_config
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File does not exist: assets/nf-core-genepal_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-genepal_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-genepal_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genepal/genepal/.github/workflows/awstest.yml
included_configs - included_configs

✅ 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: 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/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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: 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-genepal_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/WorkflowGenepal.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 - .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/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/linting_comment.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
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
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/csv'
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: download_pipeline.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
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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - EGGNOGMAPPER found in conf/base.config and Nextflow scripts.
base_config - REPEATMASKER_REPEATMASKER found in conf/base.config and Nextflow scripts.
base_config - REPEATMODELER_REPEATMODELER found in conf/base.config and Nextflow scripts.
base_config - EDTA_EDTA found in conf/base.config and Nextflow scripts.
base_config - BRAKER3 found in conf/base.config and Nextflow scripts.
base_config - GENEPALREPORT found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
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
version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

nf-core/tools version 3.0.2
Run at 2024-12-20 00:28:53

Fixed post-liftoff merge

Fixed a crash due to short introns

liamlelievre and others added 30 commits December 4, 2024 13:00

Add EXTRACT_CDS feature to GFF_STORE workflow

c8667c9

Update gff_store.nf

dbebd7a

Correct indents and whitespaces

Update gff_store.nf

203af9b

add EXTRACT_CDNA to gff_store.nf

13fe4e9

add GFF_STORE:EXTRACT_CDNA to modules.config

c7bf40b

Update gff_store.nf

f0699a6

Add cdna and cds outputs to output.md

563bd13

Add notes about cdna and cds update to CHANGELOG.md

79befa5

Added liamlelievre to contributors - README.md

47e2cf3

Update output.md

2a118be

removed end of line "/"

Added v0.6.0 notes to CHANGELOG.md

216225c

removed trailing whitespace gff_store.nf

74cd2b2

Removed trailing whitespace - modules.config

81871ff

rename params - modules.config

3f898b0

params.add_attrs_to_proteins_fasta to params.add_attrs_to_gffread_fastas

Rename params - nextflow.config

5af18c8

Rename params.add_attrs_to_proteins_fasta to params.add_attrs_to_gffread_fastas

Added code contributors

841ea02

Run nf-test successfully in minimal and stub

e05a469

Run nf-test successfully in minimal and stub, renamed attr, updated docs

d2ff47e

Merge branch 'main' into add-gffread-feature

2bcab04

Add attributes option for -F -D to cds and cdna

d21d70e

Fixed linting issues

9be84b2

Updated snapshot

767239a

Fixed nextflow-setup version

e042615

Fixed indent

43742fb

Merge pull request #119 from liamlelievre/add-gffread-feature

17673f7

Add gffread EXTRACT_CDNA and EXTRACT_CDS feature to outputs

Fixed an issue where TSEBRA failed because LIFTOFF lifted non-protein…

fb9a0f4

… coding genes

Updated snapshots

87cf1dd

Updated changelog

7d1f318

Merge pull request #122 from Plant-Food-Research-Open/patch/121

e1cceba

Fixed TSEBRA failure issue

Fixed issues in genepal-report

b9b7d37

GallVp added 8 commits December 10, 2024 16:08

Merge pull request #126 from Plant-Food-Research-Open/patch/124

496ff62

Fixed issues in genepal-report

Added parameter filter_genes_by_aa_length

3114adb

Updated snapshots

d694431

Added test to verify that GFFREAD can filter mRNA by CDS length

0f7784c

Updated snapshots

f980772

Updated README and snapshot

ab3ae37

Added 1 to filter_genes_by_aa_length to exclude stop codon from filte…

c65ebaa

…r length

Merge pull request #127 from Plant-Food-Research-Open/feat/filter_gen…

9759882

…es_by_aa_length Added parameter filter_genes_by_aa_length

GallVp added 4 commits December 16, 2024 13:28

Fixed post-liftoff merge

fa28176

Merge pull request #130 from Plant-Food-Research-Open/fix/mergefail

2a0c7a2

Fixed post-liftoff merge

Fixed short intron crash

3459b40

Merge pull request #131 from Plant-Food-Research-Open/fix/short_intron

d069633

Fixed a crash due to short introns

GallVp merged commit 023488c into main Dec 20, 2024
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Release candidate for 0.6.0 #129

Release candidate for 0.6.0 #129

GallVp commented Dec 15, 2024

github-actions bot commented Dec 15, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Release candidate for 0.6.0 #129

Release candidate for 0.6.0 #129

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GallVp commented Dec 15, 2024

PR checklist

github-actions bot commented Dec 15, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Dec 15, 2024 •

edited

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