Ann has done this mostly in ticket

https://jira.bioviz.org/browse/IGBF-3790

For NF Core, I do not see any newer versions beyond the V 3.14 that is already in place on the cluster.

I checked the latest list of nf-core piplines here: https://nf-co.re/pipelines/

Using the search text entry box at the top of the page, I searched the term "transcriptome".

There is currently a "dev" (under development?) pipeline called "denovotranscript". Its description (as of today) is:

nf-core/denovotranscript is a bioinformatics pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq. It takes a samplesheet and FASTQ files as input, perfoms quality control (QC), trimming, assembly, redundancy reduction, pseudoalignment, and quantification. It outputs a transcriptome assembly FASTA file, a transcript abundance TSV file, and a MultiQC report with assembly quality and read QC metrics.

The pipeline can perform transcript assembly using Trinity (not good) or rnaSPAdes (better, as per the latest results from Brandon Bendickson and Robert Reid).

I would say that this pipeline could be a great option for us.

I advise the following next steps:

1) Join the "denovotranscript" Slack channel - see https://github.com/nf-core/denovotranscript/tree/dev for details
2) Read posts there to get familiar with the channel.
3) Ask the channel if the pipeline is ready for us to try it, considering that we haven't used it before and are "newbies." Is this "dev" pipeline ready for use by the likes of us?
4) Put together the various parameter files needed to run the pipelne. Note that for us, we need to make sure that any intron size related parameters, especially the maximum intron size, are set properly. (I'm not sure if this would be an issue for this application because the de novo assemblies do not need to align transcripts onto a genome assembly.)
5) Run the pipeline.
6) Assess results by aligning the assembled transcript sequences against a suitable reference genome - SL4 or SL5 if assembling tomato data.

Request for Robert Reid:

Please read the comments and close this ticket, if you see fit!

This might be worthwhile to explore.
Definitely worth doing the slack channel component.

I would call this low priority as it is mostly a repeat of this summer's pipeline which is nearing completion.
One Huge advantage to getting a nextflow de novo pipeline set up will be the ease of repeating the experiments or running new datasets. So worthwhile.