test(spaceranger): Add stub for mkref

modules/nf-core/spaceranger/mkref/main.nf

@@ -41,4 +41,37 @@ process SPACERANGER_MKREF {
         spaceranger: \$(spaceranger -V | sed -e "s/spaceranger spaceranger-//g")
     END_VERSIONS
     """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "SPACERANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    """
+    mkdir -p $reference_name
+
+    touch ${reference_name}/genome.fa
+    touch ${reference_name}/genome.fa.fai
+    touch ${reference_name}/genes.gtf.gz
+    touch ${reference_name}/reference.json
+    touch ${reference_name}/Genome
+    touch ${reference_name}/SA
+    touch ${reference_name}/SAindex
+    touch ${reference_name}/chrLength.txt
+    touch ${reference_name}/chrName.txt
+    touch ${reference_name}/chrNameLength.txt
+    touch ${reference_name}/chrStart.txt
+    touch ${reference_name}/exonGeTrInfo.tab
+    touch ${reference_name}/exonInfo.tab
+    touch ${reference_name}/geneInfo.tab
+    touch ${reference_name}/sjdbInfo.txt
+    touch ${reference_name}/sjdbList.fromGTF.out.tab
+    touch ${reference_name}/sjdbList.out.tab
+    touch ${reference_name}/transcriptInfo.tab
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        spaceranger: \$(spaceranger -V | sed -e "s/spaceranger spaceranger-//g")
+    END_VERSIONS
+    """
 }