Merge pull request #298 from drpatelh/fixes

export CONDA_PREFIX into container when using Singularity and Apptainer

CHANGELOG.md

@@ -20,6 +20,7 @@ Special thanks to the following for their contributions to the release:
 - [Alexandru Mizeranschi](https://github.com/nicolae06)
 - [Alexander Blaessle](https://github.com/alexblaessle)
 - [Lukas Forer](https://github.com/lukfor)
+- [Matt Niederhuber](https://github.com/mniederhuber)
 - [Maxime Garcia](https://github.com/maxulysse)
 - [Sateesh Peri](https://github.com/sateeshperi)
 - [Sebastian Uhrig](https://github.com/suhrig)
@@ -54,6 +55,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #294](https://github.com/nf-core/fetchngs/pull/294) - Replace mermaid diagram with subway map
 - [PR #295](https://github.com/nf-core/fetchngs/pull/295) - Be less stringent with test expectations for CI
 - [PR #296](https://github.com/nf-core/fetchngs/pull/296) - Remove params.outdir from tests where required and update snapshots
+- [PR #298](https://github.com/nf-core/fetchngs/pull/298) - `export CONDA_PREFIX` into container when using Singularity and Apptainer
 
 ### Software dependencies
 

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 \\

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