Version 0.4.0
Pre-release
Pre-release
What's Changed
Added
- Added
orthofinder_annotations
param - Added
FASTA_GFF_ORTHOFINDER
sub-workflow - Added evaluation by BUSCO #41
- Included common tax ids for eggnog mapper #27
- Implemented hierarchical naming scheme: geneI.tJ, geneI.tJ.exonK, geneI.tJ.cdsK #19, #34
- Now sorting list of bam and list of fastq before cat to avoid resume cache misses
- Allowed BAM files for RNA evidence #3
- Added
GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES
sub-workflow for splice type statistics #11 - Changed
orthofinder_annotations
from FASTA/GFF to protein FASTA #43 - Added param
enforce_full_intron_support
to turn on/off strict model purging by TSEBRA #21 - 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 - Added a script to automatically check module version updates
- Reduced
BRAKER3
threads to 8 #55 - Now the final annotations are stored in the
annotations
folder #53 - Now a single
fasta
file can be directly specified forprotein_evidence
eggnogmapper_db_dir
is not a required parameter anymoreeggnogmapper_tax_scope
is now set to 1 (root div) by default- Added a
test
profile based on public data - Added parameter
add_attrs_to_proteins_fasta
to enable/disable addition of decoded gff attributes to proteins fasta #58 - 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
- Now
REPEATMASKER
GFF output is saved viaCUSTOM_RMOUTTOGFF3
#54 - Added
benchmark
column to the input sheet and usedGFFCOMPARE
to perform benchmarking #63 - Added
SEQKIT_RMDUP
to detect duplicate sequence and wrap the fasta to 80 characters - Updated parameter section labels for annotation and post-annotation filtering #64
- Updated modules and sub-workflows
Fixed
- Fixed BRAKER spellings #36
- Fixed liftoff failure when lifting off from a single reference #40
- Added versions from GFF_STORE sub-workflows #33
Dependencies
- NextFlow!>=23.04.4
- nf-validation=1.1.3
Deprecated
- Renamed
external_protein_fastas
param toprotein_evidence
- Renamed
fastq
param torna_evidence
- Renamed
braker_allow_isoforms
param toallow_isoforms
- Moved liftoffID from gene level to mRNA/transcript level
- Moved
version_check.sh
to.github/version_checks.sh
- Removed dependency on https://github.com/kherronism/nf-modules.git for
BRAKER3
andREPEATMASKER
modules which are now installed from https://github.com/GallVp/nxf-components.git - Removed dependency on https://github.com/PlantandFoodResearch/nxf-modules.git
- Now the final annotations are not stored in the
final
folder - Now BRAKER3 outputs are not saved by default #53 and saved under
etc
folder when enabled - Removed
local
profile. Local executor is the default when no executor is specified. Therefore, thelocal
profile was not needed. - Removed
CUSTOM_DUMPSOFTWAREVERSIONS
Full Changelog: 0.3.3...0.4.0