Liftoff possibly creating CDS with '.' in phase column?

[GallVp]

Description of the bug

CDS features with '.' in the phase column (8) is not permissible. This might be causing the following error downstream in the pipeline. An issue on the liftoff repo mentions something similar. See: agshumate/Liftoff#67

Command executed:

tsebra.py
-g eriantha_h2.clean.gtf
-e hintsfile.gff

-c tsebra-config.cfg

-o eriantha_h2.gtf
-s eriantha_h2.tsv

cat <<-END_VERSIONS > versions.yml
"PLANTFOODRESEARCHOPEN_GENEPAL:GENEPAL:FASTA_LIFTOFF:GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST:TSEBRA":
tsebra: 1.1.2.5
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:

READING GENE PREDICTION: [eriantha_h2.clean.gtf]

READING EXTRINSIC EVIDENCE: [hintsfile.gff]

BUILD OVERLAP GRAPH

Traceback (most recent call last):
File "/usr/local/bin/tsebra.py", line 235, in
main()
File "/usr/local/bin/tsebra.py", line 97, in main
graph.build()
File "/usr/local/bin/overlap_graph.py", line 185, in build
if self.compare_tx_cds(tx1, tx2):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/bin/overlap_graph.py", line 207, in compare_tx_cds
coords += [c + [int(phase)] for phase, coord_phase in tx1.get_type_coords('CDS').items() for c in coord_phase]
^^^^^^^^^^
ValueError: invalid literal for int() with base 10: '.'

Command used and terminal output

nextflow run plant-food-research-open/genepal \
--outdir 's3://***' \
-r '0.5.0' \
-params-file params.json \
-c mmc.config \
-resume

Relevant files

No response

System information

plant-food-research-open/genepal 0.5.0

[GallVp]

In the reported version plant-food-research-open/genepal 0.5.0, this is not possible as GFFREAD is run before and after LIFTOFF. GFFREAD automatically fixes the phase column.