3 parametrize pre filtering

[jakubmajercik]

No description provided.

[dorien-er]

The integration test for Xenium data is currently failing, but should be fixed by setting --min_var_counts 1 in src/workflows/generate_qc_report/test.nf:

workflow test_xenium {

  resources_test_file = file(params.resources_test)

  output_ch = Channel.fromList([
      [
        id: "sample_one",
        input: resources_test_file.resolve("spatial_qc_sample_data/xenium_tiny.qc.h5mu"),
        run_cellbender: false,
        ingestion_method: "xenium",
        var_gene_names: "gene_ids",
        min_num_nonzero_vars: "1",
        output_html: "report.html",
        publish_dir: "test_out"
      ],
      [
        id: "sample_two",
        input: resources_test_file.resolve("spatial_qc_sample_data/xenium_tiny.qc.h5mu"),
        ingestion_method: "xenium",
        var_gene_names: "gene_ids",
        min_num_nonzero_vars: "1",
        run_cellbender: false,
        output_html: "report.html",
        publish_dir: "test_out"
      ]
    ])
 ...

[dorien-er]

Updating src/ingestion_qc/generate_html/script.sh to the following will fix unit test:

ABSOLUTE_INPUT_DATA=$(realpath $par_input_data)
ABSOLUTE_INPUT_STRUCTURE=$(realpath $par_input_structure)
ABSOLUTE_OUTPUT=$(realpath $par_output_qc_report)

cd /opt/qc_report_generator
mkdir src/data
...