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Currently you enter the file name/path and MD5sum through the UI on a per run basis. As this cannot be done until after the data is received and since files are sometimes re-organized... we need a more efficient way to update these.

For example a TripalImporter which handles a file with the following columns:

• Run Name: as it is in LIMS
• file name: file name including full path
• md5sum: the checksum for the file.

This importer should update the information which already exists, as well as, add any new information. There is no need to warn on update.

To be made Tripal v3 compatible this module simply needs the dependency in the .info file changed from tripal_core to tripal.

This is due to the main change between Tripal v2 and Tripal v3 being Nodes => Entities and this module does not interact with Tripal Nodes.

We've had another request for additional dropdown options from Rob:

For this run

• the 'Technology' - is 'NovaSeq6000 (Illumina)'
• the 'Library Type' - we used a 'CRISPRclean Ribosomal RNA Depletion (Jumpcode Genomics)'

While you are at it - we will be doing some sequencing in the near future using the new 'PacBio Revio' - so maybe add that to 'Technology' as well.

Only nucleotide (ATCGatcg) can pass index sequence validation, but we want to allow 4 oligos, separated by comma, in one index now.
Adding ',' to index sequence validation then.

Kirstin expressed a need for a dynamic list of all the germplasm we have sequence data for. This would be in addition to the current search and needs to have both search/browse functionality. It is most useful for nanopore and exome capture data. She had mentioned having a list per technology nested under the current search.

This should be implemented using the chado_search_api.

At the top of a Sequencing Run page (for example: node/1782743), the breadcrumbs show Home >> Projects. It would be more intuitive if instead of 'Projects' the user could go back to the Sequencing Run Search.

This request came up in response to #12 as if you are searching for the data we have for a given germplasm you also need to know the amount and quality of that data. However, it will also be good feedback for the wetlab.

The plan to is make a TripalImporter for quality data which will have at least the following required columns:

• Run name (must match existing record in lims)
• Sample Name (must match sample name in specified run)
• Sample Accession (could be looked up?)
• Number of Bases
• Number of Reads
• Depth

As for display, the current thought is to make a separate table to display quality information on the run page with the preference being a tabbed interface between sample info and quality.

From Larissa and Rob, adapter sequences for LR-11 are different from "GBS 96-plex", so it is better to have a new drop-down selection: "NextFlex 96-plex".

Rob needs to add the 10X data to LIMS which will require updates for Library type and index type.

New Library Type will be "10X Chromium".
New Index Type will be "10X Chromium index set".

In the Raw Sequence Search, I receive no results for using either filter for "Oxford Nanopore: ligation" or "Oxford Nanopore: rapid". There is currently data with these library types which should result from the search, which you can see by specifying "Oxford Nanopore" for Technology.

It's been tested that duplicated names in column run_name are allowed in table lims_seqrun, HOWEVER, the lims_importer needs run name to be unique to update information of filepath and md5sum.