Question: Custom scheme Midnight-IDT/V2
fwa93 opened this issue · 2 comments
What happened?
There is a V2 for Midnight-IDT. I tried to use the custom_schema flag but could not get it to work. How would a typical command look like when you use the custom scheme flag?
My command: nextflow run epi2me-labs/wf-artic/ –r v0.3.25 -c cpu_conf.config --fastq fastq_pass/ --sample_sheet sample_sheet_wf_artic.csv --out_dir v20_v2 -profile singularity --custom_scheme custom_primer_schemes/Midnight-IDT/V2/ --artic_threads 20 --pangolin_threads 40 --threads 80 --min_len 150 --max_len 1200 --scheme_name SARS-CoV-2
I have these two files in the V2 dir:
SARS-CoV-2.scheme.bed SARS-CoV-2.reference.fasta
Operating System
ubuntu 20.04
Workflow Execution
Command line
Workflow Execution - EPI2ME Labs Versions
No response
Workflow Execution - CLI Execution Profile
Singularity
Workflow Version
v0.3.25
Relevant log output
.
Hi @fwa93,
We'll update the repository to include this primer scheme. In the meantime using a custom scheme is the way to go like you have attempted. Your command looks OK - but I would suggest using the full path to the custom scheme directory and not a relative one. Let me know if that works - if you could post the error message that would be great.
Thanks
Matt
Adding Midnight-IDT v2 to wf-artic in v0.3.30