From bdd8159c535e740ae6b831de6f28cc2ceda14ba9 Mon Sep 17 00:00:00 2001 From: Anthony Underwood Date: Tue, 11 Jan 2022 21:10:26 +0000 Subject: [PATCH] Add functionality to handle vbz compression (#1197) * 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 --- modules/artic/minion/main.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/artic/minion/main.nf b/modules/artic/minion/main.nf index ce04fcc8..ed3c64d7 100644 --- a/modules/artic/minion/main.nf +++ b/modules/artic/minion/main.nf @@ -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 \\