search

epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
Other
47 stars 34 forks source link

Question: Custom scheme Midnight-IDT/V2 #81

Closed fwa93 closed 1 year ago

fwa93 commented 1 year ago

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

.
mattdmem commented 1 year ago

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

mattdmem commented 1 year ago

Adding Midnight-IDT v2 to wf-artic in v0.3.30