bccdc-phl / 16s-nf Goto Github PK

We're currently taking the sample ID from the input fasta filename:

...but when we use multi-fasta files, we want to take the ID from the fasta header.

It would be nice to include one or more 16S rRNA sequences in the repository to be used as testing examples when setting up the pipeline. This will streamline pipeline setup and Conda installation for users following the 16S SOP.

As a starting point, I will aim to add a single rRNA sequence with corresponding annotations to a new test folder.

Allow the blast results to be filtered based on one or more regular expressions (regexes). This can be used to filter out 'uncultured' results, or other similar categories of results that are not wanted in the final blast output.

In order to flexibly support multiple regexes, they can be supplied in a multi-line file, with one line per regex. The file should be supplied using the --filter_regexes flag, and it should be optional.

We've adopted a strategy for tracking database versioning and other metadata that involves storing a metadata.json file alongside the blast database files.

At minimum, the metadata.json file must include these fields:

{
  "version": "1.1",
  "date": "2020-06-24"
}

...though additional fields may be present (they will be ignored by this pipeline).

The version info will be included in each record of the blast results, under the fields:

database_version
database_date

In addition, the ID field of the databases.csv will be included under the field:

database_name

Database metadata should be collected by default, but it can be skipped using the --no_db_metadata flag.

The pipeline is still labeled as BCCDC-PHL/fasta-blasta

We may want to blast against multiple databases, and aggregate the outputs into a single report.

To support an arbitrary number of databases, we could pass the databases as a samplesheet (dbsheet?) like this:

ID,DBNAME,PATH
ncbi_16S,16S_ribosomal_RNA,/path/to/ncbi/2023-09-19_1.1_16S_ribosomal_RNA
silva,SSURef_NR99_tax_silva_trunc,/path/to/silva/2020-08-24_138.1_SSURef_NR99_tax_silva_trunc