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vib-singlecell-nf / vsn-pipelines

A repository of pipelines for single-cell data in Nextflow DSL2
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[BUG] Error: Cannot append SCENIC loom to SCope loom because the IDs do not match #363

Open iUser1234 opened 3 years ago

iUser1234 commented 3 years ago

Hi,

I've been trying to get the multiple SCENIC iterations to work with my mouse data, but I have been running into a few issues that I've been able to fix. Nevertheless, I am posting the issue here now as I have gotten completely stuck. When I run the single_sample_scenic entry, it consistently aborts with the error statement "Cannot append SCENIC loom to SCope loom because the IDs do not match". I'm not exactly sure what causes this as the input file should be the same. I can run the "single_sample" entrypoint sucessfully.

To Reproduce Steps to reproduce the behavior:

  1. Configure with these options:
nextflow config vib-singlecell-nf/vsn-pipelines \
    -profile loom,single_sample_scenic,scenic_multiruns,scenic_use_cistarget_motifs,mm10,docker \
    > mouse_data.vsn-pipelines.complete.config
  1. Run using this entry point:
nextflow -C mouse_data.vsn-pipelines.complete.config \
    run vib-singlecell-nf/vsn-pipelines \
    -entry single_sample_scenic
  1. See error:
Cannot append SCENIC loom to SCope loom because the IDs do not match.

 -- Check script '/Users/****/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/./src/scenic/main.nf' at line: 194 or see '.nextflow.log' file for more details

Please complete the following information:

Additional context I ran into two other issues prior to this, one in which I had to make a small change in the source code to get the single_sample to work, and another in which I had to download the mouse transcription factors myself and change the specified directory in the config file, although I'm not sure if the latter was done on purpose.