millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

Artic vbz compression (#1205)

Browse source 
* 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
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 1 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
modules/artic/minion/main.nf
View file

@ -43,7 +43,7 @@ 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"
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