Running hadge on multiple samples

The pipeline is able to run on multiple samples. In this scenario, the shared parameters for input data are retrieved from a sample sheet using params.multi_sample, which is set to null by default.

Sample sheet

• The sample sheet should contain a column called sampleId for unique sample IDs assigned to each sample.

• The sample sheet (example file see the Resources section below) must contain different columns depending on the mode and methods you want to run.

  • hashing mode:

    sampleId	rna_matrix_raw	rna_matrix_filtered	hto_matrix_raw	hto_matrix_filtered
    sample1
    sample2

  • genetic mode: Set the value to “None” if the input data, for example, vcf_donor, is not available, similar to the single-sample mode. Do not forget to include the columns for HTO and RNA count matrices if params.generate_anndata or params.generate_mudata is enabled.

    sampleId	bam	bam_index	barcodes	nsample	celldata	vcf_mixed	vcf_donor
    sample1
    sample2

  • rescue mode:

    sampleId	rna_matrix_raw	rna_matrix_filtered	hto_matrix_raw	hto_matrix_filtered	bam	bam_index	barcodes	nsample	celldata	vcf_mixed	vcf_donor
    sample1
    sample2

• The remaining parameters for each process are specified in the nextflow.config file, just like when demultiplexing a single sample.

• There is a distinction between running on a single sample and running on multiple samples. When processing multiple samples, the pipeline only permits a single value for each process parameter, whereas in the case of a single sample, multiple values separated by commas are allowed.

Output

When running the pipeline on multiple samples, the pipeline output will be found in the folder "$projectDir/$params.outdir/$sampleId/$params.mode.

Resources

There is an example sample sheet for multi_sample mode.