Bioinformatics
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      What do I do if the pipeline says it cannot find my STAR reference when it clearly exists?

      Failure mode


      the `NF:CURIOSEEKER:PRIMARY_READ2:STAR_ALIGN (Mouse_spleen_1M)` Process dies after three retries with the following error:


      The genome file (and the entire root of the reference) is indeed accessible at `/reference/indexes/curio/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/genomeParameters.txt`. As the user can validate and confirm permissions



      Affected storage:


      Solution 1

      1. Add a param to `nextflow.config` that contains an argument string that should be passed to any process that uses the container and need to access the affected storage system (see below and the highlighted line 33 in screenshot below):



      1. In the definition .nf file for each process that was erroring, add the following directive (see below and highlighted line 10 for in screenshot below):



      Solution 2

      Place all input files and direct both --outdir and -work-dir to the storage system that the container has access to.