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Merged
marchoeppner merged 1 commit into from
Dec 16, 2022
Merged

Updating documentation #5

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5 changes: 3 additions & 2 deletions docs/usage.md
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Expand Up @@ -54,7 +54,7 @@ A regular expression pointing to a set of paired-end fastQ files.
nextflow run ikmb/hla --reads '/path/to/*_R{1,2}_001.fastq.gz'
```

### `--tools`
### `--tools` [ default: hisat,xhla,hlascan ]

This pipeline supports several competing tool chains for HLA calling. Specify them with this option as a comma-separated list.

Expand All @@ -65,8 +65,9 @@ nextflow run ikmb/hla --samples Samples.csv --tools 'hisat,xhla,optitype'
Supported tools:

* [xHLA](https://github.com/humanlongevity/HLA) (xhla)
* [Hisat-genotype](https://daehwankimlab.github.io/hisat-genotype/) (hisat) SLOW!!
* [Hisat-genotype](https://daehwankimlab.github.io/hisat-genotype/) (hisat) Slow on anything other than targetted sequencing!
* [Optitype](https://github.com/FRED-2/OptiType) (optitype)
* [HLAscan](https://github.com/SyntekabioTools/HLAscan) (hlascan)

### `--run_name`

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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -8,7 +8,7 @@ params {

email = null

tools = "xhla,optitype"
tools = "xhla,hisat,hlascan"

plaintext_email = false

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