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Add functionality to handle vbz compression (#1197)

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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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Anthony Underwood 2022-01-11 21:10:26 +00:00 committed by GitHub
parent e751e5040a
commit bdd8159c53
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modules/artic/minion/main.nf
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@ -43,7 +43,10 @@ process ARTIC_MINION {
summary = ""
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"
"""
$hd5_plugin_path
artic \\
minion \\
$args \\