add docs on external tools, update CHANGELOG

CHANGELOG.md

@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#157](https://github.com/nf-core/epitopeprediction/pull/157) - Add JSON config for external prediction tools
 - [#161](https://github.com/nf-core/epitopeprediction/pull/161) - Add rank values for prediction threshold (as default) and parameter `use_affinity_thresholds` to use affinity thresholds instead [#160](https://github.com/nf-core/epitopeprediction/issues/160)
 - [#165](https://github.com/nf-core/epitopeprediction/pull/165) - Add tools to full size test, add MHC class II to MHCnuggets test
-- [#166](https://github.com/nf-core/epitopeprediction/pull/166) - Add support for the non-free `NetMHC` family tools `NetMHCpan 4.1`, `NetMHCII 2.2`(Darwin), `NetMHCII 2.3`, `NetMHCIIpan 4.0`, and `NetMHCIIpan 4.1`
+- [#166](https://github.com/nf-core/epitopeprediction/pull/166) - Add support for additional non-free `NetMHC` family tools
 - [#168](https://github.com/nf-core/epitopeprediction/pull/168) - Add parameters to specify MHC class II peptide length (`max_peptide_length_class2` and `min_peptide_length_class2`)
 - [#170](https://github.com/nf-core/epitopeprediction/pull/170) - Add `binder` column (binder to any specified MHC allele)
 

docs/usage.md

@@ -95,6 +95,19 @@ work                # Directory containing the nextflow working files
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
 
+### Running the pipeline with external prediction tools
+
+The pipeline can be used with external prediction tools that cannot be provided with the pipeline due to license restrictions.
+
+Currently we do support prediction tools of the `netMHC` family. Please refer to the [parameter docs](https://nf-co.re/epitopeprediction/latest/parameters#tools) for the list of supported tools. If one of the external tools is specified, the path to the corresponding tarball has to be specified.
+When using `conda`, the parameter `--netmhc_system` (if the default value `linux` is not applicable) must also be specified.
+
+A typical command is as follows:
+
+```console
+nextflow run nf-core/epitopeprediction --input samplesheet.csv -profile docker --tools netmhcpan-4.1 --netmhciipan_path /path/to/netMHCIIpan-4.0.Linux.tar --outdir <OUTDIR>
+```
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. After this, it will use the cached version if available - even if the pipeline has been updated since. To ensure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:

nextflow_schema.json

@@ -197,22 +197,22 @@
                 "netmhcpan_path": {
                     "type": "string",
                     "default": "None",
-                    "description": "To use the 'netmhcpan' tool, specify the path to the original software tarball for NetMHCpan 4.0 (Linux) here."
+                    "description": "To use the 'netmhcpan' tool, specify the path to the original software tarball for NetMHCpan 4.0 here."
                 },
                 "netmhc_path": {
                     "type": "string",
                     "default": "None",
-                    "description": "To use the 'netmhc' tool, specify the path to the original software tarball for NetMHC 4.0 (Linux) here."
+                    "description": "To use the 'netmhc' tool, specify the path to the original software tarball for NetMHC 4.0 here."
                 },
                 "netmhciipan_path": {
                     "type": "string",
                     "default": "None",
-                    "description": "To use the 'netmhciipan' tool, specify the path to the original software tarball for NetMHCIIpan 3.1 (Linux) here."
+                    "description": "To use the 'netmhciipan' tool, specify the path to the original software tarball for NetMHCIIpan 3.1 here."
                 },
                 "netmhcii_path": {
                     "type": "string",
                     "default": "None",
-                    "description": "To use the 'netmhcii' tool, specify the path to the original software tarball for NetMHCII 2.2 (Linux) here."
+                    "description": "To use the 'netmhcii' tool, specify the path to the original software tarball for NetMHCII 2.2 here."
                 }
             }
         },