[GA2] make additional file available

The VGP project generates a large amount of data, some of which is available in the GenomeArk bucket on Jetstream2. It would be great to display some of these files—such as pretext files—on the GenomeArk webpage. Additionally, it would be useful to make other files available as selectable options when configuring a workflow.

# These files are

## Files create from official assembly releases

For the VGP Phase 1 assemblies, we’ve started generating 2bit-compressed assembly files and RepeatModeler family files (while also storing the corresponding FASTA files). These resources could be very useful for downstream analyses, as they require considerable computational effort to produce. Some decions for these files:
* [ ] How should these be provided during workflow configuration?
* New data selector type?
* Do we provide Galaxy with download links to the files, or do we mount the storage system directly to Galaxy?”
* Should the fasta files be select-able? Maybe not since we will have the data multiple times then.
* [ ] Should we provide links to them for people who easily want to download them?

## Raw Data

Within each species folder, you can find the raw data used to generate the assemblies. This data can also be valuable for various downstream analyses. While some of it is available from ENA or SRA, not all datasets are accessible through those repositories.

### Genomic Data
The data is located at species/{ORGANISM_NAME}/{ToLID}/genomic_data/ in the GenomeArk bucket, where several different data types are stored.
* [ ] Arima (fastq.gz)
* [ ] illumina (fastq.gz)
* [ ] pacbio_hifi (bam, fastq.gz)

We also have data considered as Legacy Genomic Data:
* [ ] 10x (fastq.gz)
* [ ] bionano (bnx.gz, cmap.gz)
* [ ] ont (bam, fastq.gz)
* [ ] ont_duplex (bam, fastq.gz)
* [ ] pacbio (bam, fastq.gz)

### Transcriptomic Data

The data is located at species/{ORGANISM_NAME}/{ToLID}/transcriptomic_data/tissue_type in the GenomeArk bucket, where several different data types are stored.
* [ ] illumina (fastq.gz)
* [ ] pacbio (bam, subreads.bam)

## Pre release assembly files

Before being submitted to NCBI, some assembly files are only available in the GenomeArk bucket (depending on which VGP partner performed the assembly). Note that these files remain accessible in the bucket even after submission. In addition to the various assembly files, this location also contains several evaluation files.

Assembly files:
* assembly curated (species/{ORGANISM_NAME}/{ToLID}/assembly_curated/)
* [ ] {genome_id}.hap1.cur.YYYYMMDD.fastq.gz
* [ ] {genome_id}.hap2.cur.YYYYMMDD.fastq.gz
* [ ] {genome_id}.hap1.cur.YYYYMMDD.pretext
* [ ] {genome_id}.hap2.cur.YYYYMMDD.pretext
* [ ] {genome_id}.alt.cur.YYYYMMDD.fasta.gz
* [ ] {genome_id}.pri.cur.YYYYMMDD.fasta.gz
* [ ] {genome_id}.alt.cur.YYYYMMDD.pretext
* [ ] {genome_id}.pri.cur.YYYYMMDD.pretext
* [ ] {genome_id}.alt.cur.pretext
* [ ] {genome_id}.pri.cur.pretext
* Uncurated Assemblies (species/{ORGANISM_NAME}/{ToLID}/assembly_{pipeline}_{ver}/)
* [ ] {genome_id}.standard.alt.YYYYMMDD.fastq.gz
* [ ] {genome_id}.standard.pri.YYYYMMDD.fastq.gz
* evalutation
* [ ] busco
* [ ] genomescope
* [ ] gfastats
* [ ] merqury
* [ ] pretext

We need to decide whether we want to make all or only some of these files available on GenomeArk2. If we do, we also need to determine how to make them available—some files may only need to be displayed, while others should be accessible for use in workflow configurations. As a starting point, we could mark the ones we plan to make available (if any).