1.0.1

What's Changed

• [GH-185] Fixed malformed STAR ALIGN command by @GallVp in #187

Full Changelog: 1.0.0...1.0.1

Version 1.0.0

What's Changed

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. nf-schema@2.5.1

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

PRs

• Bumped dev version to 1.0.0dev by @GallVp in #164
• Bump template version to 3.3.1 by @GallVp in #165
• Template update for nf-core/tools version 3.4.0 by @GallVp in #168
• Updated modules and sub-workflows by @GallVp in #169
• Updated the nf-core template to 3.4.1 by @GallVp in #170
• [GH-89] Fixed flagging of introns shorter than 10bp by @GallVp in #171
• [GH-161] Fixed failure due to invalid Fasta IDs by @GallVp in #172
• [GH-166] Fixed pipeline crash from empty lines in the prot file by @GallVp in #174
• [GH-160] Fixed crash in fasta_liftoff due to same file names by @GallVp in #175
• [GH-163] Fixed BAM sorting in STAR_ALIGN on large genomes by @GallVp in #176
• Bumped version to 1.0.0 by @GallVp in #177
• Fixed memory limit calc. for star/align by @GallVp in #179
• Added a --tags parameter by @GallVp in #180
• Added param --strict_fasta_id_validation by @GallVp in #181
• Release candidate for 1.0.0 by @GallVp in #178

Full Changelog: 0.7.2...1.0.0

Version 0.7.2

What's Changed

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. nf-schema@2.2.0

PRs

• Now using agat_sp_complement_annotations.pl to merge Liftoff and BRAKER models by @GallVp in #154

Full Changelog: 0.7.1...0.7.2

Version 0.7.1

What's Changed

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. nf-schema@2.2.0

PRs

• Gene models from BRAKER with invalid ORF(s) are now removed by @GallVp in #152

Full Changelog: 0.7.0...0.7.1

Version 0.7.0

What's Changed

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. nf-schema@2.3.0

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

PRs

• Added gene feature naming by @jasonshiller in #136
• Added parameter append_genome_prefix_to_feature_ids by @GallVp in #137
• Added a unit test for filter_genes_by_aa_length on gffread by @GallVp in #141
• Updated nf-core template to 3.2.0 by @GallVp in #142
• Fixed an issue where filter_genes_by_aa_length was not correctly by @GallVp in #143
• Updated modules and sub-workflows by @GallVp in #144
• Prepared a release candidate for 0.7.0 by @GallVp in #145
• Fixed linting issues by @GallVp in #147
• Updated date to get aound PR checks issue by @GallVp in #149
• Fixed busco snapshots by @GallVp in #150
• Version 0.7.0 by @GallVp in #148

New Contributors

• @jasonshiller made their first contribution in #136

Full Changelog: 0.6.0...0.7.0

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