Cafe go and get data nf tests working

Eco-Flow · May 3, 2024 · 2d1ac47 · 2d1ac47
1 parent c3c32cc
commit 2d1ac47
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Showing 4 changed files with 8 additions and 13 deletions.
diff --git a/bin/cafe_go.pl b/bin/cafe_go.pl
@@ -314,7 +314,7 @@
 
 print $out1 "Total_HOGs_significant\tExpansion_HOGs_significant\tContraction_HOGs_significant\tExpansion_genes_significant\tContraction_genes_significant\tExpansion_HOGs_total\tContraction_HOGs_total\n";
 
-foreach my $species2 (keys %SPECIES_TOTAL){
+foreach my $species2 (sort keys %SPECIES_TOTAL){
     print $out1 "$species2\t$SPECIES_TOTAL{$species2}";
     if ($SPECIES_EXPANSION{$species2}){
         print $out1 "\t$SPECIES_EXPANSION{$species2}";

diff --git a/tests/modules/local/cafe_go.nf.test b/tests/modules/local/cafe_go.nf.test
@@ -30,10 +30,8 @@ nextflow_process {
 
             //Assert snapshot of the two main output files
             assert snapshot(
-              path("${launchDir}/${params.outdir}/cafe_go/Go_summary_neg.pdf"),
-              path("${launchDir}/${params.outdir}/cafe_go/Go_summary_pos.pdf"),
-              path("${launchDir}/${params.outdir}/cafe_go/TopGO_Pval_barplot_Bombus_affinis.neg.txt_TopGo_results_ALL.tab.pdf"),
-              path("${launchDir}/${params.outdir}/cafe_go/TopGO_Pval_barplot_Bombus_affinis.pos.txt_TopGo_results_ALL.tab.pdf"),
+              path("${launchDir}/${params.outdir}/cafe_go/CAFE_summary.txt"),
+              path("${launchDir}/${params.outdir}/cafe_go/versions.yml")
             ).match("cafe_go") 
         }
     }

diff --git a/tests/modules/local/cafe_go.nf.test.snap b/tests/modules/local/cafe_go.nf.test.snap
@@ -1,15 +1,13 @@
 {
     "cafe_go": {
         "content": [
-            "Go_summary_neg.pdf:md5,741d23b669ee48d0a1a342e3f61a6fbc",
-            "Go_summary_pos.pdf:md5,fe9e2a9c8d1f4c230c4617fb76564748",
-            "TopGO_Pval_barplot_Bombus_affinis.neg.txt_TopGo_results_ALL.tab.pdf:md5,aba8c67927da9696fc958b4b7ba5e130",
-            "TopGO_Pval_barplot_Bombus_affinis.pos.txt_TopGo_results_ALL.tab.pdf:md5,3580af1c7b66146a11e2646b358f74a2"
+            "CAFE_summary.txt:md5,b6cbf4877b159864b97d514273b4ab67",
+            "versions.yml:md5,acfc3dae393e700a8add474731579ae8"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-02T22:50:02.180953"
+        "timestamp": "2024-05-03T12:01:52.31372"
     }
 }
diff --git a/tests/modules/local/getdata.nf.test.snap b/tests/modules/local/getdata.nf.test.snap
@@ -1,13 +1,12 @@
 {
     "getdata": {
         "content": [
-            "amellifera_eg_gene.go.txt:md5,45469f5443f8a0e6623b8fa2ac554e13",
-            "amellifera_eg_gene.fasta:md5,6a6b20f3e0bb91079cc3426288285397"
+            "amellifera_eg_gene.go.txt:md5,45469f5443f8a0e6623b8fa2ac554e13"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-02T22:24:34.596451"
+        "timestamp": "2024-05-03T11:38:32.886613"
     }
 }