Add singularity.registry = 'quay.io' for tests

modules/nf-core/fastqc/main.nf

@@ -29,7 +29,11 @@ process FASTQC {
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
-    fastqc $args --threads $task.cpus $renamed_files
+
+    fastqc \\
+        $args \\
+        --threads $task.cpus \\
+        $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/gatk4/applybqsrspark/main.nf

@@ -31,7 +31,9 @@ process GATK4_APPLYBQSR_SPARK {
         avail_mem = (task.memory.mega*0.8).intValue()
     }
     """
-    gatk --java-options "-Xmx${avail_mem}M" ApplyBQSRSpark \\
+    gatk \\
+        --java-options "-Xmx${avail_mem}M" \\
+        ApplyBQSRSpark \\
         --input $input \\
         --output ${prefix}.${input.getExtension()} \\
         --reference $fasta \\

tests/config/nextflow.config

@@ -13,6 +13,7 @@ process {
 
 if ("$PROFILE" == "singularity") {
     singularity.enabled = true
+    singularity.registry = 'quay.io'
     singularity.autoMounts = true
 } else if ("$PROFILE" == "conda") {
     conda.enabled = true
@@ -38,5 +39,5 @@ conda { createTimeout = "120 min" }
 includeConfig 'test_data.config'
 
 manifest {
-    nextflowVersion = '!>=22.10.1'
+    nextflowVersion = '!>=23.04.0'
 }

tests/config/nf-test.config

@@ -14,6 +14,7 @@ process {
 profiles {
     singularity {
         singularity.enabled = true
+        singularity.registry = 'quay.io'
         singularity.autoMounts = true
     }
     conda {
@@ -44,5 +45,5 @@ conda { createTimeout = "120 min" }
 includeConfig 'test_data.config'
 
 manifest {
-    nextflowVersion = '!>=22.10.1'
+    nextflowVersion = '!>=23.04.0'
 }