Update nf-tests

nf-core · Feb 8, 2024 · 474feb0 · 474feb0
1 parent 14a1507
commit 474feb0
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Showing 4 changed files with 39 additions and 12 deletions.
diff --git a/nf-test.config b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "tests/"
 
     // nf-test directory including temporary files for each test
-    workDir "/tmp"
+    workDir ".nf-test"
 
     // location of library folder that is added automatically to the classpath
     libDir "lib/"

diff --git a/tests/test.nf.test b/tests/test.nf.test
@@ -18,11 +18,22 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    path("$outputDir/diamond/database.dmnd"),
-                    path("$outputDir/kaiju/database.fmi"),
-                    ).match() },
+                        path("$outputDir/diamond/database.dmnd"),
+                        path("$outputDir/kaiju/database.fmi"),
+                        path("$outputDir/malt/malt-build.log").readLines().last().contains('Peak memory'),
+                        path("$outputDir/malt/malt_index/index0.idx"),
+                        path("$outputDir/malt/malt_index/ref.db"),
+                        path("$outputDir/malt/malt_index/ref.idx"),
+                        path("$outputDir/malt/malt_index/ref.inf"),
+                        path("$outputDir/malt/malt_index/taxonomy.idx"),
+                        path("$outputDir/malt/malt_index/taxonomy.map"),
+                        path("$outputDir/malt/malt_index/taxonomy.tre")
+                    ).match()
+                },
                 { assert new File("$outputDir/pipeline_info/software_versions.yml").exists() },
-                { assert new File("$outputDir/multiqc/multiqc_report.html").exists() }
+                { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
+                { assert path("$outputDir/malt/malt_index/table0.db").exists() },
+                { assert path("$outputDir/malt/malt_index/table0.idx").exists() },
             )
         }
     }

diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
@@ -2,8 +2,20 @@
     "test_profile": {
         "content": [
             "database.dmnd:md5,9d57aa88cd1766adfda8360876fc0e4f",
-            "database.fmi:md5,54fd89f5e4eab61af30175e8aa389598"
+            "database.fmi:md5,54fd89f5e4eab61af30175e8aa389598",
+            true,
+            "index0.idx:md5,876139dc930e68992cd2625e08bba48a",
+            "ref.db:md5,335d4c8c7367999d79bef51882809f5f",
+            "ref.idx:md5,a07f93cdce0154d3e05e8cacc5480a3a",
+            "ref.inf:md5,446275f4f879e2b115e983db7c9ced18",
+            "taxonomy.idx:md5,309f2a558c08f551fc939e749fd42fd8",
+            "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0",
+            "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e"
         ],
-        "timestamp": "2023-12-14T12:55:54.070245428"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T10:59:42.922218767"
     }
 }
diff --git a/workflows/createtaxdb.nf b/workflows/createtaxdb.nf
@@ -111,7 +111,6 @@ workflow CREATETAXDB {
         ch_versions = ch_versions.mix(CAT_CAT_DNA.out.versions.first())
     }
 
-    // TODO: COPY COMPRESSION PROCEDURE ABOVE BUT FOR AA!
     // TODO: Possibly need to have a modification step to get header correct to actually run with kaiju...
     // TEST first!
     // docs: https://github.com/bioinformatics-centre/kaiju#custom-database
@@ -144,8 +143,6 @@ workflow CREATETAXDB {
     // MODULE: Run DIAMOND/MAKEDB
     //
 
-    // TODO
-    // - nf-test
     if ( params.build_diamond  ) {
         DIAMOND_MAKEDB ( CAT_CAT_AA.out.file_out, params.prot2taxid, params.nodesdmp, params.namesdmp )
         ch_versions = ch_versions.mix(DIAMOND_MAKEDB.out.versions.first())
@@ -173,8 +170,6 @@ workflow CREATETAXDB {
             ch_malt_mapdb = file(params.malt_mapdb)
         }
 
-        ch_input_for_malt
-
         if ( params.malt_sequencetype == 'Protein') {
             ch_input_for_malt = ch_prepped_aa_fastas.map{ meta, file -> file }
         } else {
@@ -209,6 +204,15 @@ workflow CREATETAXDB {
         ch_multiqc_logo.toList()
     )
     multiqc_report = MULTIQC.out.report.toList()
+
+    emit:
+    versions            = CUSTOM_DUMPSOFTWAREVERSIONS.out.versions
+    multiqc_report_html = MULTIQC.out.report
+    diamond_database    = DIAMOND_MAKEDB.out.db
+    kaiju_database      = KAIJU_MKFMI.out.fmi
+    malt_database       = MALT_BUILD.out.index
+
+
 }
 
 /*