From 4e22bc961084688ce9a0c6f8d1d564b70b7af912 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 2 Apr 2022 15:20:36 +0200
Subject: [PATCH] fix: force UTF-8 in different locale?

---
 nextflow.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 9f3b103..588c0cf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -158,7 +158,8 @@ if (!params.igenomes_ignore) {
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
 
 env {
-    PYTHONNOUSERSITE = 1
+    PYTHONNOUSERSITE = '1'
+    PYTHONUTF8       = '1'  // MetaPhlAn3 may fail with a UnicodeDecodeError if the locale is not set appropriately.
     R_PROFILE_USER   = "/.Rprofile"
     R_ENVIRON_USER   = "/.Renviron"
     JULIA_DEPOT_PATH = "/usr/local/share/julia"