From e196431842b039cbf5c299c7a3e568f6a3e30e33 Mon Sep 17 00:00:00 2001
From: Florian De Temmerman <florian.detemmerman@pixelgen.com>
Date: Thu, 11 Jan 2024 13:24:36 +0100
Subject: [PATCH] disable docker.runOptions -u and -g to workaround container
 issue

---
 nextflow.config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index d3384f50..f6193e5a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -154,7 +154,8 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
-        docker.runOptions      = '-u $(id -u):$(id -g)'
+        // Disabled this to deal with libpysal temporary directory issue
+        // docker.runOptions      = '-u $(id -u):$(id -g)'
     }
     arm {
         docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
@@ -271,7 +272,7 @@ manifest {
     description     = """Pipeline for analysis of Molecular Pixelation assays"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '1.1.0dev'
+    version         = '1.1.0dev'
     // TODO: Use zenodo DOI once available
     doi             = '10.1101/2023.06.05.543770'
 }