Apply nf-test suggestions in ska/distance

nf-core · Feb 6, 2025 · ca4c914 · ca4c914
1 parent f3b6aa3
commit ca4c914
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Showing 5 changed files with 328 additions and 60 deletions.
diff --git a/modules/nf-core/ska/distance/main.nf b/modules/nf-core/ska/distance/main.nf
@@ -44,12 +44,12 @@ process SKA_DISTANCE {
     def output_dist  = task.ext.args =~ "-d" ? "" : "touch ${prefix}.distances.tsv"
     def output_clust = task.ext.args =~ "-c" ? "" : "touch ${prefix}.clusters.tsv"
     // this is not a complete criterion for this output but it is good enough
-    def output_dot   = task.ext.args =~ "-S" || sketch_files.size > 1 ? "touch ${prefix}.dot" : ""
+    def output_dot   = task.ext.args =~ "-S" || sketch_files.size() > 1 ? "touch ${prefix}.dot" : ""
     """
     $output_dist
     $output_clust
     # this is not how this works but it's the best we can do without knowing the input content
-    for i in {1..${sketch_files.size}}
+    for i in {1..${sketch_files.size()}}
     do
         touch ${prefix}.cluster\${i}.txt
     done

diff --git a/modules/nf-core/ska/distance/tests/main.nf.test b/modules/nf-core/ska/distance/tests/main.nf.test
@@ -27,7 +27,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.distances[0][1]).csv(sep:"\t").sort(),
+                    path(process.out.cluster_list[0][1]).csv(sep:"\t").sort(),
+                    process.out.dot
+                ).match() }
             )
         }
 
@@ -62,30 +67,44 @@ nextflow_process {
     test("sarscov2 - pfal - list") {
 
         setup {
-            """
-            echo "sarscov2_reduced.skf" > sketch_list.txt
-            echo "plasmodium_reduced.skf" >> sketch_list.txt
-            wget https://raw.githubusercontent.com/nf-core/test-datasets/modules/genomics/sarscov2/genome/ska/sarscov2_reduced.skf
-            wget https://raw.githubusercontent.com/nf-core/test-datasets/modules/genomics/eukaryotes/plasmodium_falciparum/ska/plasmodium_reduced.skf
-            """
+            run("WGET", alias: "WGET1") {
+                script "modules/nf-core/ska/distance/wget.nf"
+                process {
+                """
+                input[0] = params.modules_testdata_base_path + 'genomics/sarscov2/genome/ska/sarscov2_reduced.skf'
+                input[1] = "sarscov2_reduced.skf"
+                """
+                }
+            }
+
+            run("WGET", alias: "WGET2") {
+                script "modules/nf-core/ska/distance/wget.nf"
+                process {
+                """
+                input[0] = params.modules_testdata_base_path + 'genomics/eukaryotes/plasmodium_falciparum/ska/plasmodium_reduced.skf'
+                input[1] = "plasmodium_reduced.skf"
+                """
+                }
+            }
         }
 
         when {
             process {
                 """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    [],
-                    [file("sketch_list.txt", checkIfExists: true)]
-                ]
+                input[0] = WGET1.out.outfile.mix(WGET2.out.outfile).map {it -> it.toString()}.collectFile(name: 'samples.txt', newLine: true).map { it -> [['id': 'test'], [], it] }
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.distances[0][1]).csv(sep:"\t").sort(),
+                    path(process.out.cluster_list[0][1]).csv(sep:"\t").sort(),
+                    process.out.dot
+                ).match() }
             )
         }