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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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[Bug]: Problem with a custom scheme #78

Closed michallaz closed 1 year ago

michallaz commented 1 year ago

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['PrimerID'].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 commented 1 year ago

Hello - you can't use _alt.

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

Matt