Version 0.6.0

What's Changed

Added

1. Added cDNA and CDS outputs to <OUTPUT_DIR>/annotations/ directory #118
2. Added parameter add_attrs_to_proteins_cds_fastas
3. Added parameter filter_genes_by_aa_length with default set to 24 which allows removal of genes with ORFs shorter than 24 #125

Fixed

1. Fixed an issue where TSEBRA failed because LIFTOFF lifted non-protein coding genes #121
2. Switched branch name from master to main in the GHA CIs
3. Fixed an issue in genepal_report.Rmd which caused the pangene matrix plot to fail when the number of clusters exceeded 65536 #124
4. Fixed an issue where GENEPALREPORT process failed due to OOM kill signal from SLURM #123
5. Fixed an issue where Gff merge after liftoff failed when one of the Gff files did not contain any genes
6. Fixed an issue where gxf_fasta_agat_spaddintrons_spextractsequences crashed due to short introns #89

Dependencies

1. Nextflow!>=24.04.2
2. nf-schema@2.1.1

Deprecated

1. Removed parameter add_attrs_to_proteins_fasta

PRs

• Add gffread EXTRACT_CDNA and EXTRACT_CDS feature to outputs by @liamlelievre in #119
• Fixed TSEBRA failure issue by @GallVp in #122
• Fixed issues in genepal-report by @GallVp in #126
• Added parameter filter_genes_by_aa_length by @GallVp in #127
• Fixed post-liftoff merge by @GallVp in #130
• Fixed a crash due to short introns by @GallVp in #131
• Release candidate for 0.6.0 by @GallVp in #129

New Contributors

• @liamlelievre made their first contribution in #119

Full Changelog: 0.5.0...0.6.0

Version 0.5.0

What's Changed

Added

1. Added MultiQC #65
2. Updated nf-core template to 3.0.2 #66
3. Integrated nf-test into pipeline CI #68
4. Updated the flowchart #87
5. Added a large test dataset for the test_full profile #90
6. Now .gff.gz and .gff3.gz inputs are also allowed for the benchmark column in --input
7. Now removing liftoff genes with any intron shorted than 10bp #89
8. Now also removing rRNA and tRNA after liftoff as the downstream logic in the pipeline can not correctly handle these
9. Now skipping FastQC by default #98
10. Added an HTML report #44
11. Added content type as text/html for the MultiQC and genepal reports
12. Added sra-tools for RNASeq data download #102

Fixed

1. Now using ${meta.id}_trim as prefix for FASTQC files
2. Updated citations to include DOIs
3. Fixed a bug where FASTQ versions were not correctly captured
4. Now using the correct out channel from STAR_ALIGN. This bug was introduced by a module update during the development of this version #74
5. Fixed OrthoFinder results copy failure on AWS #108

Dependencies

1. Nextflow!>=24.04.2
2. nf-schema@2.1.1

Deprecated

1. Resource parameters have been removed: max_memory, max_cpus, max_time
2. Removed a number of unnecessary parameters: monochromeLogs, config_profile_contact, config_profile_url, validationFailUnrecognisedParams, validationLenientMode, validationSchemaIgnoreParams, validationShowHiddenParams, validate_params
3. Removed extra_fastp_args and replaced it with fastp_extra_args
4. Removed and replaced skip_fastp and skip_fastqc with fastp_skip and fastqc_skip #82

PRs

• Updated nf-core template to 3.0.2 by @GallVp in #67
• Integrated nf-test into pipeline CI by @GallVp in #71
• Updated docs to include -r flag by @GallVp in #72
• Now using the correct out channel from STAR_ALIGN by @GallVp in #78
• Removed extra_fastp_args and replaced it with fastp_extra_args by @GallVp in #81
• Removed and replaced skip_fastp and skip_fastqc by @GallVp in #83
• Updated the flowchart by @GallVp in #88
• Added a large dataset for test_full by @GallVp in #91
• Now skipping FastQC by default by @GallVp in #99
• Added an HTML report by @GallVp in #100
• Added content type as text/html for the MultiQC and genepal reports by @GallVp in #101
• Added sra-tools for RNASeq data download by @GallVp in #103
• Fixed minor issues in report modules by @GallVp in #106
• Fixed OrthoFinder results copy failure on AWS by @GallVp in #109
• Added doi and bumped version by @GallVp in #110
• Removed an unnecessary config block by @GallVp in #111
• Fixed linting issues by @GallVp in #113
• Added GeneMark license info by @GallVp in #114
• Candidate for 0.5.0 by @GallVp in #112

Full Changelog: 0.4.0...0.5.0

Version 0.4.0

What's Changed

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

Full Changelog: 0.3.3...0.4.0

Version 0.3.3

What's Changed

Full Changelog: 0.3.2...0.3.3

Added

1. Added a stub test to evaluate the case where an assembly is soft masked but has no annotations

Fixed

1. Fixed a bug where is_masked was ignored by the pipeline
2. Fixed a bug in param validation which allowed specification of braker_hints without braker_gff3

Dependencies

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

Deprecated

Version 0.3.2

What's Changed

• Now removing comments from FASTA file before feeding it to BRAKER by @GallVp in #32

Full Changelog: 0.3.1...0.3.2

Version 0.3.1

What's Changed

• Increased time limit for longer tasks by @GallVp in #30

Full Changelog: 0.3.0...0.3.1

Version 0.3.0

What's Changed

Commit history: v0.2...0.3.0

Added

1. Added changelog and semantic versioning
2. Changed license to MIT
3. Updated .editorconfig
4. Moved .literature to test/ branch
5. Renamed pangene_local to local_pangene
6. Renamed pangene_pfr to pfr_pangene
7. Added versioning checking
8. Updated github workflow to use pre-commit instead of prettier and editorconfig check
9. Added central singularity cache dir for pfr config
10. Added SORTMERNA_INDEX before SORTMERNA
11. Fixed sample contamination bug introduced by file.simpleName
12. Now using empty files for stub testing in CI
13. Now BRAKER can be skipped by including BRAKER outputs from previous runs in the target_assemblies param
14. Added gffcompare to merge liftoff annotations
15. Renamed samplesheet param to fastq
16. Now using assemblysheet in combination with nf-validation for assembly input
17. Added nextflow_schema.json
18. Now using nf-validation to validate fastqsheet provided by params.fastq
19. Moved manifest.config and reporting_defaults.config content to nextflow.config
20. Now using a txt file for params.external_protein_fastas
21. Now using nf-validation for params.liftoff_annotations
22. Now using nf-validation for all the parameters
23. Added PURGE_BREAKER_MODELS sub-workflow
24. Added GFF_EGGNOGMAPPER sub-workflow
25. Now using a custom version of GFFREAD which supports meta and fasta
26. Now using TSEBRA to purge models which do not have full intron support from BRAKER hints
27. Added params eggnogmapper_evalue and eggnogmapper_pident
28. Added PURGE_NOHIT_BRAKER_MODELS sub-workflow
29. Now merging BRAKER and liftoff models before running eggnogmapper
30. Added GFF_MERGE_CLEANUP sub-workflow
31. Now using description field to store notes and textual annotations in the gff files
32. Now using mRNA in place of transcript in gff files
33. Now eggnogmapper_purge_nohits is set to false by default
34. Added GFF_STORE sub workflow
35. external_protein_fastas and eggnogmapper_db_dir are not mandatory parameters
36. Added contributors
37. Add a document for the pipeline parameters
38. Updated pfr_pangene and pfr/profile.config
39. Now using local tests/stub files for GitHub CI
40. Now removing iso-forms left by TSEBRA using AGAT_SPFILTERFEATUREFROMKILLLIST
41. Added pyproject.toml
42. Now using PFAMs from eggnog if description is '-'

Fixed

1. Removed liftoff models with valid_ORF=False
2. Updated license text to include 'Copyright (c) 2024 The New Zealand Institute for Plant and Food Research Limited'

Dependencies

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

Deprecated