Question about --spaln_taxon

[Warahb14]

Description of feature

Hi, I'm trying to include protein sequences from many related species of worms for training protein-coding genes (I have no target protein sequence for target species), and after ran Nextflow (nf-core/genomeannotator) I got error message about --spaln_taxon.

Error

-[nf-core/genomeannotator] Pipeline completed with errors-
ERROR ~ A process input channel evaluates to null -- Invalid declaration `val spaln_taxon`

 -- Check script '/user/.nextflow/assets/nf-core/genomeannotator/subworkflows/local/spaln_align_protein.nf' at line: 38 or see '.nextflow.log' file for more details

I am unsure how many --spaln_taxon models should be specified when protein sequences from multiple related species are used. Is it possible to provide more than one taxon?

[marchoeppner]

Hi, I think this pipeline is currently considered "abandonware" ;) There is a slightly more recent version in my personal repo here:
https://github.com/marchoeppner/genomeannotator

As for your question, spaln_taxon refers to the splicing model used for the alignments, so it should match your species of interest (and yes, only one value is allowed).

Supported values can be found here, in column 2 (if memory serves):
https://github.com/ogotoh/spaln/blob/master/table/gnm2tab

Your species probably won't be in that list, so just pick whatever is closest.

[ewels]

For visibility: there is discussion in the nf-core Slack about revamping this pipeline and @OlivierCoen taking over responsibility as maintainer. See this thread for details.

@OlivierCoen has something similar already here: https://github.com/OlivierCoen/genome_annotator - @GallVp and @nschan also both have their own pipelines and an interest, so hopefully with all of this existing material we can bring nf-core/genomeannotator back to life 🧟 😄

Hijacking the GitHub issue sorry so let's not spam further, if folks want to discuss more then please jump onto the nf-core slack #genomeannotatorchannel 🙏🏻

[Warahb14]

Hi, I think this pipeline is currently considered "abandonware" ;) There is a slightly more recent version in my personal repo here: https://github.com/marchoeppner/genomeannotator

As for your question, spaln_taxon refers to the splicing model used for the alignments, so it should match your species of interest (and yes, only one value is allowed).

Supported values can be found here, in column 2 (if memory serves): https://github.com/ogotoh/spaln/blob/master/table/gnm2tab

Your species probably won't be in that list, so just pick whatever is closest.

Thank you so much :):)

[Warahb14]

For visibility: there is discussion in the nf-core Slack about revamping this pipeline and @OlivierCoen taking over responsibility as maintainer. See this thread for details.

@OlivierCoen has something similar already here: https://github.com/OlivierCoen/genome_annotator - @GallVp and @nschan also both have their own pipelines and an interest, so hopefully with all of this existing material we can bring nf-core/genomeannotator back to life 🧟 😄

Hijacking the GitHub issue sorry so let's not spam further, if folks want to discuss more then please jump onto the nf-core slack #genomeannotatorchannel 🙏🏻

Appreciate your useful guide, I'll explore it.