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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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[Bug]: epi2me-labs/wf-artic v0.3.22 EPI2ME Labs V4.1.2 workflow primer scheme selection #76

Closed PWSmit closed 1 year ago

PWSmit commented 1 year ago

What happened?

Issue persist with earlier reported bug #73, even with updated version (clean install W10 PC). Demo data test run works. have tested various schemes, all results in error.

Also, noticed 2 more scheme versions that are not functional when selected (ONT/V1 and ONT/V4.1) resulting in notification after the run has started that those are not valid options (also not shown in log file below).
image

Operating System

Windows 10

Workflow Execution

EPI2ME Labs desktop application

Workflow Execution - EPI2ME Labs Versions

V4.1.2

Workflow Execution - CLI Execution Profile

Docker

Workflow Version

0.3.22

Relevant log output

Input Options
  fastq          : /mnt/c/data/20230223_covid19_run110/20230223_covid19_run110/20230223_1433_MN38468_FAV30369_f1b6f2dc/fastq_pass
Primer Scheme Selection
  scheme_version : ARTIC/V4.1
  scheme_dir     : /mnt/c/Users/KioskEpi2me/AppData/Local/EPI2MELabs/app-4.1.2/primer_schemes
Output Options
  out_dir        : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/64e0aeae4bde7ea987c3c73bf0b7a241a8b9492dbcf6aafeffe33d15022b3c21/instances/wf-artic_313964cd-c181-4596-b05b-effcef0b263a/output
Advanced Options
  artic_threads  : 8
  min_len        : 150
  max_len        : 400
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-artic for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-artic v0.3.22.
--------------------------------------------------------------------------------
      ------------------------------------
      Available Primer Schemes:
      ------------------------------------

  Name      Version
  SARS-CoV-2    ARTIC/V1    
  SARS-CoV-2    ARTIC/V2    
  SARS-CoV-2    ARTIC/V3    
  SARS-CoV-2    ARTIC/V4    
  SARS-CoV-2    ARTIC/V4.1  
  SARS-CoV-2    Midnight-IDT/V1 
  SARS-CoV-2    Midnight-ONT/V1 
  SARS-CoV-2    Midnight-ONT/V2 
  SARS-CoV-2    Midnight-ONT/V3 
  SARS-CoV-2    NEB-VarSkip/v1a 
  SARS-CoV-2    NEB-VarSkip/v1a-long    
  SARS-CoV-2    NEB-VarSkip/v2  
  SARS-CoV-2    NEB-VarSkip/v2b 
      ------------------------------------

No such file: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/64e0aeae4bde7ea987c3c73bf0b7a241a8b9492dbcf6aafeffe33d15022b3c21/workflows/epi2me-labs/wf-artic/data/mnt/c/Users/KioskEpi2me/AppData/Local/EPI2MELabs/app-4.1.2/primer_schemes
 -- Check script '/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/64e0aeae4bde7ea987c3c73bf0b7a241a8b9492dbcf6aafeffe33d15022b3c21/workflows/epi2me-labs/wf-artic/main.nf' at line: 548 or see '/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/64e0aeae4bde7ea987c3c73bf0b7a241a8b9492dbcf6aafeffe33d15022b3c21/instances/wf-artic_313964cd-c181-4596-b05b-effcef0b263a/nextflow.log' file for more details
mattdmem commented 1 year ago

Thanks for this - looking into it

mattdmem commented 1 year ago

Fix coming in v0.3.23 today hopefully!

mattdmem commented 1 year ago

@PWSmit v0.3.23 is released - we'd welcome your feedback!

PWSmit commented 1 year ago

Had to remove the workflow as updating didn't work but it runs now. thanks!