Reduce storage used by tests

nf-core · Feb 16, 2024 · 7218318 · 7218318
1 parent 147b318
commit 7218318
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Showing 4 changed files with 67 additions and 63 deletions.
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -9,16 +9,18 @@ nextflow_pipeline {
     test("Parameters: default") {
         when {
             params {
-                outdir                  = "$outputDir"
-                mash_screen_min_score   = 0.5
-                genomad_min_score       = 0.01
-                genomad_max_fdr         = 1
-                genomad_disable_nn      = true
-                genomad_sensitivity     = 0.1
-                checkv_minimal_db       = true
-                iphop_partial_test      = true
-                max_cpus                = 4
-                max_memory              = '15.GB'
+                outdir                      = "$outputDir"
+                mash_screen_min_score       = 1
+                mash_screen_winner_take_all = true
+                genomad_min_score           = 0.01
+                genomad_max_fdr             = 1
+                genomad_disable_nn          = true
+                genomad_sensitivity         = 0.1
+                checkv_minimal_db           = true
+                checkv_min_length           = 3000
+                iphop_partial_test          = true
+                max_cpus                    = 4
+                max_memory                  = '15.GB'
             }
         }
 

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
diff --git a/workflows/phageannotator/tests/skip_genomad.nf.test b/workflows/phageannotator/tests/skip_genomad.nf.test
@@ -20,24 +20,26 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir                  = "$outputDir"
-                skip_genomad            = true
-                mash_screen_min_score   = 0.5
-                genomad_min_score       = 0.01
-                genomad_max_fdr         = 1
-                genomad_disable_nn      = true
-                genomad_sensitivity     = 0.1
-                checkv_minimal_db       = true
-                iphop_partial_test      = true
+                outdir                      = "$outputDir"
+                skip_genomad                = true
+                mash_screen_min_score       = 1
+                mash_screen_winner_take_all = true
+                genomad_min_score           = 0.01
+                genomad_max_fdr             = 1
+                genomad_disable_nn          = true
+                genomad_sensitivity         = 0.1
+                checkv_minimal_db           = true
+                checkv_min_length           = 25000
+                iphop_partial_test          = true
             }
         }
 
         then {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(workflow.out).match() },
-                { assert path("${outputDir}/VirusLifestyle/bacphlip/all_samples_anicluster_representatives.fna.bacphlip").readLines().size() == 156 },
-                { assert path("${outputDir}/VirusAbundance/coverm/contig/all_samples_alignment_results.tsv").readLines().size() == 156 }
+                { assert path("${outputDir}/VirusLifestyle/bacphlip/all_samples_anicluster_representatives.fna.bacphlip").readLines().size() == 9 },
+                { assert path("${outputDir}/VirusAbundance/coverm/contig/all_samples_alignment_results.tsv").readLines().size() == 9 }
             )
         }
     }

diff --git a/workflows/phageannotator/tests/skip_genomad.nf.test.snap b/workflows/phageannotator/tests/skip_genomad.nf.test.snap