Allow no reads to start

[nbx0]

reformat.sh crashes snakemake if run on an empty fastq. Empty fastq can be generated from cat step when fastq_pass/barcodeXX directory exists and there are no fastqs within it. I assume the directory was created by Minknow but that all of barcodeXX reads were put in fastq_fail. Not sure...

[kristinelacek]

I have handling for this in the ONT on-prem snakemake. Basically when the yaml is created, empty fastq_pass dirs are never included in the DAG. The script prints out all the failed barcodes and includes them in the "analyses beginning" email notification. This is, I assume, not the intended behavior for a GUI like MIRA since we still want to show said samples in our figures/etc?

[nbx0]

Correct. We still want the sampleID to show up in the IRMA summary table, but will have 0 reads to start… From: Kristine Lacek ***@***.***> Sent: Wednesday, June 21, 2023 11:03 AM To: CDCgov/MIRA ***@***.***> Cc: Rambo Martin, Benjamin (CDC/DDID/NCIRD/ID) ***@***.***>; Author ***@***.***> Subject: Re: [CDCgov/MIRA] Allow no reads to start (Issue #19) I have handling for this in the ONT on-prem snakemake. Basically when the yaml is created, empty fastq_pass dirs are never included in the DAG. The script prints out all the failed barcodes and includes them in the "analyses beginning" email notification. This is, I assume, not the intended behavior for a GUI like MIRA since we still want to show said samples in our figures/etc? — Reply to this email directly, view it on GitHub<#19 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJPHCXTJJ2CJTYXUS4W676TXMMELPANCNFSM6AAAAAAZIIIMQE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[kristinelacek]

nbx0/spyne#32

[kristinelacek]

This MR pulls my empty barcode dir branch into illumina-flu branch (big boy)