Jacques Dainat
The tool/pipeline you ran does not originate from https://github.com/NBISweden/GAAS repository but from this repository (https://github.com/NBISweden/pipelines-nextflow/). I transferred your issue here to be better monitored
The annotation_preprocessing new pipeline does not filter out the contigs less than 1000 nucleotides
Interesting, GAAS has the same release since 2020 (v1.2), the script should continue to work in the same way.
> I'm going to see if we can use some students to make nf-core modules for ours. That would be awesome
Sounds fair. I would suggest to keep transcript ÌD because in case of isoform would be difficult to guess from which transcript the CDS comes from: ``` >CDS:ENSP00000431562 transcript=ENST00000399012 gene=gene:ENSG00000182378...
CDS chunks may share the same identifier, in this case how to differentiate the different extracted CDS chunks? I guess we should add in the descritption the chunck number or...
Yes. A CDS is a single feature that can exist over multiple genomic locations (in case of multi exons genes). So several CDS features (lines in the GFF) can be...
Seems to be related to #416
AGAT Libraries are not reached. Probably installation didn't work well. The `make test` probably did not work, isn't it? Feel free to re-open the issue if necessary.
It sounds the code involved in your issue has been updated after v1.0.0. Could you give a try with the latest version (v1.4.0)? You may go more straithgforward: ``` agat...
Could you share a sample of the data used?