From 06494258f6b5d307c5a9c2b43e6f6dc0cec2edb2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 29 Feb 2024 11:49:47 +0000
Subject: [PATCH] export CONDA_PREFIX into container when using Singularity and
 Apptainer

---
 modules/local/aspera_cli/main.nf | 5 +++++
 nextflow.config                  | 8 --------
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/modules/local/aspera_cli/main.nf b/modules/local/aspera_cli/main.nf
index de78a7b2..b38d17c0 100644
--- a/modules/local/aspera_cli/main.nf
+++ b/modules/local/aspera_cli/main.nf
@@ -18,8 +18,11 @@ process ASPERA_CLI {
 
     script:
     def args = task.ext.args ?: ''
+    def conda_prefix = ['singularity', 'apptainer'].contains(workflow.containerEngine) ? "export CONDA_PREFIX=/usr/local" : ""
     if (meta.single_end) {
         """
+        $conda_prefix
+
         ascp \\
             $args \\
             -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\
@@ -36,6 +39,8 @@ process ASPERA_CLI {
         """
     } else {
         """
+        $conda_prefix
+
         ascp \\
             $args \\
             -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\
diff --git a/nextflow.config b/nextflow.config
index 0b2abf8c..bb6b6b79 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -70,14 +70,6 @@ try {
 // Workflow specific configs
 includeConfig './workflows/sra/nextflow.config'
 
-// Load nf-core/fetchngs custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/fetchngs.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/fetchngs profiles: ${params.custom_config_base}/pipeline/fetchngs.config")
-// }
-
 profiles {
     debug {
         dumpHashes             = true