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Update usage.md
johnoooh Aug 29, 2024
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nikhil Sep 10, 2024
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## Samplesheet input

You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a tsv file with 4 columns, and a header row as shown in the examples below.
You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a csv file with 4 columns, and a header row as shown in the examples below.

```bash
--input '[path to samplesheet file]'
```

```csv title="samplesheet.csv"
sample maf facets_hisens_cncf hla_file
tumor_normal temp_test_somatic_unfiltered.maf facets_hisens.cncf.txt winners.hla.txt
sample,maf,facets_hisens_cncf,hla_file
tumor_normal,temp_test_somatic_unfiltered.maf,facets_hisens.cncf.txt,winners.hla.txt
```

| Column | Description |
| ------------------------------------- | -------------------------------------------------- |
| `sample` | Custom sample name. |
| `maf` | The path to a maf output by the TEMPO pipeline. |
| `facets_hisens_cncf` | The path to the hisens cncf file output by facets. |
| `hla_file` A hla file from polysolver | |
| Column | Description |
| -------------------- | -------------------------------------------------- |
| `sample` | Custom sample name. |
| `maf` | The path to a maf output by the TEMPO pipeline. |
| `facets_hisens_cncf` | The path to the hisens cncf file output by facets. |
| `hla_file` | A hla file from polysolver |

An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.

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