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