[Bug]: Problem with a custom scheme

[michallaz]

What happened?

Hi,
I've tried to run the pipeline using nextflow with the custom_scheme option. During execution the following error occurred ( from *alignreport.er file):

Traceback (most recent call last):
File "/home/epi2melabs/conda/bin/align_trim", line 10, in
sys.exit(main())
File "/home/epi2melabs/conda/lib/python3.8/site-packages/artic/align_trim.py", line 342, in main
overlap_trim(args)
File "/home/epi2melabs/conda/lib/python3.8/site-packages/artic/align_trim.py", line 149, in overlap_trim
scheme, pair, side = b['Primer_ID'].split('_')
ValueError: too many values to unpack (expected 3)

I guess, this is because primers in my bed file have names like nCoV-2019_21_RIGHT_alt. So is there a workaround to use the pipeline with the primers' names like this?

Operating System

ubuntu 20.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - CLI Execution Profile

Singularity

Workflow Version

wf-artic v0.3.24-g6674df0

Relevant log output

None

[mattdmem]

Hello - you can't use _alt.

I would just make primer 21 the total region covered by 21 and 21_alt.

Matt