Delimeters for Genomic Addres

[sgsutcliffe]

Description of the bug

Right now, gasnomenclature does not work as expected, or has some issues if a delimeter for the genomic address besides the default ".".

GAS call is supposed to be flexible in the output, in that a delimeter other than the default can be set by using --gm_delimiter but the expected behavior of a command like:

nextflow run main.nf -profile docker,test --outdir results --gm_delimiter -

Still gives an output with the delimeter as the default "." which might be a GAS issue.

In addition, the tool is supposed to be able to accept address in the samplesheet with none "." characters but this is currently not the case. For example a samplesheet using:

sample,mlst_alleles,address
sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json,
sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1-1-1
sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1-1-1
sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1-1-2

Causes an error. Though it was due to the schema for address not including anything besides "."

gasnomenclature/assets/schema_input.json

Line 25 in 39c8c16

"pattern": "^\\d+(\\.\\d+)*$",

However when I changed the pattern to "pattern": "^\\d+([_.-]\\d+)*$", it still fails. I think this is due to an issue with GAS 0.1.3
as the error looks like:

Error something went wrong with cluster assignment. check error messages ["Genomic address too short for samples: ['sample1', 'sample2', 'sample3'] based on {0: 10.0, 1: 5.0, 2: 0.0}"]

And when I run GAS with the file files I get the same thing.

In the PR 31 we also made it so the addresses in the database and samplesheet must have the same delimeter output by GAS but that does not break anything because right now gasnomenclature can only handle the delimeter "."

Command used and terminal output

No response

Relevant files

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System information

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