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Update usage docs to specify NetMHC 4.2bstatic and NetMHCIIpan 4.3e as only supported versions #322

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jonasscheid merged 3 commits into from
Dec 31, 2025
Merged

Update usage docs to specify NetMHC 4.2bstatic and NetMHCIIpan 4.3e as only supported versions #322

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Initial plan
Copilot Dec 31, 2025
feac646
Update usage.md to specify only supported NetMHC versions
Copilot Dec 31, 2025
0e5d47e
Improve readability of NetMHC documentation
Copilot Dec 31, 2025
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9 changes: 7 additions & 2 deletions docs/usage.md
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Expand Up @@ -99,7 +99,12 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c

### Running the pipeline with NetMHC

The pipeline also aims to support the most recent NetMHCpan and NetMHCIIpan versions. If one of the external tools is specified, the path to the corresponding tarball has to be specified. See the [Download section](https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/) of NetMHCpan. When using `conda`, the parameter `--netmhc_system` (if the default value `linux` is not applicable) must also be specified.
The pipeline supports NetMHCpan 4.2bstatic and NetMHCIIpan 4.3e. If one of the external tools is specified, the path to the corresponding tarball has to be specified. See the download sections for [NetMHCpan-4.2](https://services.healthtech.dtu.dk/services/NetMHCpan-4.2/) and [NetMHCIIpan-4.3](https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.3/).

When using `conda`, the parameter `--netmhc_system` must also be specified if the default value `linux` is not applicable.

> [!IMPORTANT]
> Only the specific versions `netMHCpan-4.2bstatic.Linux.tar.gz` and `netMHCIIpan-4.3e.Linux.tar.gz` are supported, as the pipeline validates these tarballs via checksum to ensure integrity.

A typical command is as follows:

Expand All @@ -113,7 +118,7 @@ nextflow run nf-core/epitopeprediction \
--max_peptide_length_classI 12 \
--min_peptide_length_classII 12 \
--max_peptide_length_classII 25 \
--netmhcpan_path /path/to/netMHCpan-4.1b.Linux.tar.gz \
--netmhcpan_path /path/to/netMHCpan-4.2bstatic.Linux.tar.gz \
--netmhciipan_path /path/to/netMHCIIpan-4.3e.Linux.tar.gz \
```

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