Issues with Cas9 workflow: pipeline:pack_files_into_sample_dirs

[Vtsseq]

Operating System

Windows 10

Other Linux

No response

Workflow Version

v.1.1.1

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

V5.1.14

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

I am trying to analyse multiplexed Cas9 enriched sequencing data with the Epi2ME Cas9 workflow. However, the code runs until 'pipeline:pack_files_into_sample_dirs (16)' and then produces the following error: ERROR ~ Error executing process > 'pipeline:pack_files_into_sample_dirs (16)' Caused by: Not a valid path value type: java.util.ArrayList ([/mnt/c/Users/prov/epi2melabs/instances/wf-cas9_01J28TTX6Z6X38C11D3HBJMSEG/work/56/9aa8eda5d322cbe26a001358c5c804/barcode17_target_cov.tsv, /mnt/c/Users/prov/epi2melabs/instances/wf-cas9_01J28TTX6Z6X38C11D3HBJMSEG/work/56/9aa8eda5d322cbe26a001358c5c804/{meta.alias}_target_cov.tsv])

Relevant log output

{
  "name": "Launch workflow",
  "description": "Begin running a new analysis",
  "updates": [
    {
      "message": "Checking runner"
    },
    {
      "message": "Checking Windows version"
    },
    {
      "message": "WSL command exists, checking status"
    },
    {
      "message": "WSL is installed, checking version"
    },
    {
      "message": "Checking for updates to the EPI2ME distribution"
    },
    {
      "message": "WSL is ready to use."
    },
    {
      "message": "Checking Nextflow initialises"
    },
    {
      "message": "Nextflow is ready to use."
    },
    {
      "message": "All Setup tests are passing"
    },
    {
      "message": "Creating instance: peaceful_boyd"
    },
    {
      "message": "Instance created: peaceful_boyd"
    }
  ],
  "id": "01J28TTMYHJJT4H9RM7B1J42N3",
  "percentage": 100,
  "status": "COMPLETED",
  "createdAt": "2024-07-08T09:29:33.905Z",
  "updatedAt": "2024-07-08T09:29:45.054Z",
  "metadata": {
    "trace": {
      "nxfCmd": "wsl",
      "nxfArgs": [
        "-d",
        "epi2me",
        "/mnt/c/Users/prov/AppData/Local/EPI2ME/app-5.1.14/resources/nextflow-all",
        "-h"
      ],
      "nxfExitCode": "0"
    },
    "track": {
      "windowsVersion": [
        "10",
        "0",
        "19045"
      ],
      "windowsRelease": 2009,
      "wslVersion": "2.2.4",
      "workflowName": "epi2me-labs/wf-cas9",
      "instanceId": "01J28TTX6Z6X38C11D3HBJMSEG",
      "workflowVersion": "v1.1.1",
      "workflowCommit": "7811221dfbee08a8c186304487aa50399c40a2b6"
    }
  }
}

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[nrhorner]

Hi @Vtsseq. Could you paste the text from the log tab please?

[nrhorner]

HI @Vtsseq

This seems to be a bug that you have found. I think it should only occur when there are no reads mapping to the reverse strand.I'll get a fix out for this ASAP

[Vtsseq]

nextflow.log Hi nrhorner, thank you for your answer, here is the log of the instance if you still need it.

[nrhorner]

Thanks for the log. I'll let you know when that fix is release.