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plant-food-research-open/genepal: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.0.1 - [03-Feb-2026]

Fixed

  1. Fixed malformed STAR ALIGN command which caused the pipeline to fail when RNASeq data was provided #185

Dependencies

  1. Nextflow!>=25.04.0
  2. [email protected]

v1.0.0 - [05-Nov-2025]

Added

  1. Updated the nf-core template to 3.4.1
  2. Update modules and sub-workflows from nf-core/modules and GallVp/nxf-components
  3. Add parameter --tags to support nf-shard tags
  4. Added parameter --strict_fasta_id_validation to disable strict Fasta ID validation for NCBI assemblies with Fasta IDs containing periods ('.')

Fixed

  1. Fixed an issue where some genes with introns shorter than 10bp were not marked for exclusion correctly #89
  2. Fixed an issue where Fasta IDs such as >lcl|Lmh1Chr1 caused the pipeline to fail due to IDs being changed by BRAKER3 #161
  3. Fixed an issue which caused a pipeline crash where there were empty lines in the protein evidence file #166
  4. Fixed an issue where the pipeline failed when liftoff Fasta and Gff had the same file name and the Gff extension was gff3 #160
  5. Fixed an issue where STAR_ALIGN failed on large genomes in sorting the output BAM #163

Dependencies

  1. Nextflow!>=25.04.0
  2. [email protected]

Tool Updates

Tool Old Version New Version
agat 1.4.2 1.5.1
ltr_harvest_parallel 1.1 1.2
braker3 v3.0.7.6 v3.0.7.5
busco 5.8.3 6.0.0
diamond 2.1.8 2.1.12
fastp 0.24.0 1.0.1
multiqc 1.28 1.32
htslib 1.21 1.22.1
samtools 1.21 1.22.1
sortmerna 4.3.6 4.3.7
umi_tools 1.1.5 1.1.6

v0.7.2 - [06-May-2025]

Fixed

  1. Now using agat_sp_complement_annotations.pl to merge Liftoff and BRAKER models to avoid creation of iso-forms due to overlap of separate genes #153

Dependencies

  1. Nextflow!>=24.04.2
  2. [email protected]

v0.7.1 - [02-May-2025]

Fixed

  1. Gene models from BRAKER with invalid ORF(s) are now removed #151
  2. Demoted nf-schema to 2.2.0 to avoid errors with latest Nextflow versions
  3. Fixed a nextflow syntax issue in conf/modules.config

Dependencies

  1. Nextflow!>=24.04.2
  2. [email protected]

v0.7.0 - [16-April-2025]

Added

  1. Added parameter append_genome_prefix_to_feature_ids which allows the user to add genome prefixes defined in the assemblysheet to the final Gff/Fasta files #135
  2. Updated nf-core template to 3.2.0

Fixed

  1. Fixed an issue where filter_genes_by_aa_length was not correctly applied when the CDS was shorter than the transcript by replacing GFFREAD with AGAT_SPFILTERBYORFSIZE #139

Dependencies

  1. Nextflow!>=24.04.2
  2. [email protected]

Tool Updates

Tool Old Version New Version
agat 1.4.0 1.4.2
braker3 v3.0.7.5 v3.0.7.6
busco 5.7.1 5.8.3
coreutils 8.30 9.5
fastp 0.23.4 0.24.0
multiqc 1.25.1 1.28
seqkit 2.8.1 2.9.0
htslib 1.18 1.21
samtools 1.18 1.21
star 2.7.10a 2.7.11b

v0.6.0 - [20-Dec-2024]

'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. [email protected]

Deprecated

  1. Removed parameter add_attrs_to_proteins_fasta

v0.5.0 - [21-Nov-2024]

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. [email protected]

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

v0.4.0 - [04-Oct-2024]

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
  12. pipeline_info/software_versions.yml has been replaced with pipeline_info/genepal_software_mqc_versions.yml

v0.3.3 - [18-Jun-2024]

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

v0.3.2 - [13-May-2024]

Added

Fixed

  1. Increased time limit for REPEATMODELER_REPEATMODELER to 5 days
  2. Now removing comments from fasta file before feeding it to BRAKER added tests for the perl one liner
  3. Fixed CHANGELOG version check failure in version_check.sh
  4. Increased the SLURM job time limit to 14 days

Dependencies

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

Deprecated

v0.3.1 - [10-May-2024]

Added

Fixed

  1. Increased time limit for REPEATMODELER_REPEATMODELER to 3 days, REPEATMASKER to 2 days, EDTA_EDTA to 7 days, BRAKER3 to 7 days and EGGNOGMAPPER to 1 day

Dependencies

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

Deprecated

v0.3.0 - [30-April-2024]

Added

  1. Added changelog and semantic versioning
  2. Changed license to MIT
  3. Updated .editorconfig
  4. Moved .literature to test/ branch
  5. Renamed genepal_local to local_genepal
  6. Renamed genepal_pfr to pfr_genepal
  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_BRAKER_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_genepal 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