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Artic vbz compression (#1205)

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* Add functionality to handle vbz compression

In order for nanopolish to be able handle the default compression  for Mk1C Minions (vbz) it must be aware of where to find the plugin. Exporting the HDF5_PLUGIN_PATH found in the conda install (also used to make the biocontainer image) is the solution

* Make the HDF5_PLUGIN_PATH more configurable

Allow the HDF5_PLUGIN_PATH to be changed via a section in a config file e.g

```
params {
    modules {
        .....
        'nanopore_artic_minion' {
            .....
            hd5_plugin_path = '/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin'
        }
        ......
    }
}
```

* Update modules/artic/minion/main.nf

* Export HDF5_PLUGIN_PATH

The HDF5_PLUGIN_PATH variable should be exported for `artic minion` to use it

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Anthony Underwood 2022-01-13 01:05:01 +00:00 committed by GitHub
parent 4cc3921efb
commit 104f896a26
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modules/artic/minion/main.nf
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@ -43,7 +43,7 @@ process ARTIC_MINION {
summary = "" summary = ""
model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model" model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
} }
def hd5_plugin_path = task.ext.hd5_plugin_path ? "HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin" def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
""" """
$hd5_plugin_path $hd5_plugin_path