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TCP-Lab / transportome_profiler

Code to profile the expression of the transportome
GNU General Public License v3.0
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Cannot run the `heatmaps` pipeline on "test espression matrix" #27

Closed Feat-FeAR closed 10 months ago

Feat-FeAR commented 10 months ago

kerblam run heatmaps -l --profile test does not work because:

  1. espression matrix is downloaded as a TSV compressed file (expression_matrix.tsv.gz), while test espression matrix is generated as a CSV compressed file (test_expression_matrix.csv.gz), but kerblam.toml expects two CSVs... https://github.com/TCP-Lab/transportome_profiler/blob/32f40b74b63527fc45b2e7e8f7e9dbf94ca237e6/kerblam.toml#L10
  2. simply changing the TOML to 
    [data.profiles.test]
"expression_matrix.tsv.gz" = "test_expression_matrix.csv.gz"

    does not work because then metasplit crashes

    [WARNING] metasplit.core: I only read one header. This might mean you gave me the wrong delimiter.

    I think that the culprit is xsv fmt trying to format an already CSV-formatted file (albeit with TSV extension).

MrHedmad commented 10 months ago

This is fixed in ef2b50d