Candidate for 0.4.0

[GallVp]

Changes

Added

1. Added orthofinder_annotations param
2. Added FASTA_GFF_ORTHOFINDER sub-workflow
3. Added evaluation by BUSCO #41
4. Included common tax ids for eggnog mapper #27
5. Implemented hierarchical naming scheme: geneI.tJ, geneI.tJ.exonK, geneI.tJ.cdsK #19, #34
6. Now sorting list of bam and list of fastq before cat to avoid resume cache misses
7. Allowed BAM files for RNA evidence #3
8. Added GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES sub-workflow for splice type statistics #11
9. Changed orthofinder_annotations from FASTA/GFF to protein FASTA #43
10. Added param enforce_full_intron_support to turn on/off strict model purging by TSEBRA #21
11. Added param filter_liftoff_by_hints to evaluate liftoff models with TSEBRA to make sure they have the same level of evidence as BRAKER #28
12. Added a script to automatically check module version updates
13. Reduced BRAKER3 threads to 8 #55
14. Now the final annotations are stored in the annotations folder #53
15. Now a single fasta file can be directly specified for protein_evidence
16. eggnogmapper_db_dir is not a required parameter anymore
17. eggnogmapper_tax_scope is now set to 1 (root div) by default
18. Added a test profile based on public data
19. Added parameter add_attrs_to_proteins_fasta to enable/disable addition of decoded gff attributes to proteins fasta #58
20. Added a check for input assemblies. If an assembly is smaller than 1 MB (or 300KB in zipped format), the pipeline errors out before starting the downstream processes #47
21. Now REPEATMASKER GFF output is saved via CUSTOM_RMOUTTOGFF3 #54
22. Added benchmark column to the input sheet and used GFFCOMPARE to perform benchmarking #63
23. Added SEQKIT_RMDUP to detect duplicate sequence and wrap the fasta to 80 characters
24. Updated parameter section labels for annotation and post-annotation filtering #64
25. Updated modules and sub-workflows

Fixed

1. Fixed BRAKER spellings #36
2. Fixed liftoff failure when lifting off from a single reference #40
3. Added versions from GFF_STORE sub-workflows #33

Dependencies

1. NextFlow!>=23.04.4
2. nf-validation=1.1.3

Deprecated

1. Renamed external_protein_fastas param to protein_evidence
2. Renamed fastq param to rna_evidence
3. Renamed braker_allow_isoforms param to allow_isoforms
4. Moved liftoffID from gene level to mRNA/transcript level
5. Moved version_check.sh to .github/version_checks.sh
6. Removed dependency on https://github.com/kherronism/nf-modules.git for BRAKER3 and REPEATMASKER modules which are now installed from https://github.com/GallVp/nxf-components.git
7. Removed dependency on https://github.com/PlantandFoodResearch/nxf-modules.git
8. Now the final annotations are not stored in the final folder
9. Now BRAKER3 outputs are not saved by default #53 and saved under etc folder when enabled
10. Removed local profile. Local executor is the default when no executor is specified. Therefore, the local profile was not needed.
11. Removed CUSTOM_DUMPSOFTWAREVERSIONS

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0acb62b

+| ✅ 153 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 0.4.0
• 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.

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• 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
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: assets/multiqc_config.yml
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config default ignored: params.ribo_database_manifest
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• 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: assets/nf-core-genepal_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-genepal_logo_light.png
• files_unchanged - File ignored due to lint config: 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_awstest - 'awstest.yml' workflow not found: /home/runner/work/genepal/genepal/.github/workflows/awstest.yml
• multiqc_config - multiqc_config

✅ 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: 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
• 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: 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 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.eggnogmapper_tax_scope= 1
• nextflow_config - Config default value correct: params.repeat_annotator= repeatmodeler
• nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
• nextflow_config - Config default value correct: params.star_max_intron_length= 16000
• nextflow_config - Config default value correct: params.liftoff_coverage= 0.9
• nextflow_config - Config default value correct: params.liftoff_identity= 0.9
• nextflow_config - Config default value correct: params.eggnogmapper_evalue= 1e-05
• nextflow_config - Config default value correct: params.eggnogmapper_pident= 35
• nextflow_config - Config default value correct: params.allow_isoforms= true
• nextflow_config - Config default value correct: params.enforce_full_intron_support= true
• nextflow_config - Config default value correct: params.filter_liftoff_by_hints= true
• nextflow_config - Config default value correct: params.busco_lineage_datasets= eukaryota_odb10
• nextflow_config - Config default value correct: params.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 72.GB
• nextflow_config - Config default value correct: params.max_time= 7.day
• 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.publish_dir_mode= copy
• 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 - .github/.dockstore.yml matches the template
• files_unchanged - .github/CONTRIBUTING.md 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 - .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
• 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: 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 (394 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: ci.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: branch.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.
• 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.
• modules_config - conf/modules.config found and not ignored.
• modules_config - AGAT_SPFILTERFEATUREFROMKILLLIST found in conf/modules.config and Nextflow scripts.
• modules_config - SAVE_MARKED_GFF3 found in conf/modules.config and Nextflow scripts.
• modules_config - BENCHMARK 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 2024-10-04 04:14:12