update tests and snapshots

nf-core · Dec 20, 2024 · d37ee03 · d37ee03
1 parent af74838
commit d37ee03
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Showing 4 changed files with 22 additions and 10 deletions.
diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_propd_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_propd_basic.config
@@ -26,4 +26,7 @@ process {
         ext.args = {"--round_digits 5 --save_adjacency true"}
         ext.prefix = { "${meta.id}_${meta.method}" }
     }
+    withName: 'CUSTOM_FILTERDIFFERENTIALTABLE' {
+        ext.args = { meta.method == "propd" ? ["comparison2" : ">="] : []}
+    }
 }
diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test
@@ -16,6 +16,7 @@ nextflow_workflow {
 
     test("deseq2 - mouse - basic") {
         config './deseq2_basic.config'
+        tag "deseq2"
 
         when {
             workflow {
@@ -73,6 +74,7 @@ nextflow_workflow {
 
     test("limma - basic - microarray") {
         config './limma_basic_microarray.config'
+        tag "limma"
 
         setup {
             run("UNTAR") {
@@ -155,6 +157,7 @@ nextflow_workflow {
 
     test("limma - voom") {
         config './limma_voom.config'
+        tag "limma_voom"
 
         when {
             workflow {
@@ -211,6 +214,7 @@ nextflow_workflow {
 
     test("deseq2 - with transcript lengths") {
         config './deseq2_basic.config'
+        tag "deseq2_with_lengths"
 
         when {
             workflow {
@@ -302,7 +306,7 @@ nextflow_workflow {
                     file(testData.expression_test_data_dir + testData.abundance_file),
                     'propd',  // analysis method
                     1.5,      // FC threshold
-                    50        // weighted connectivity threshold
+                    100       // weighted connectivity threshold
                 ])
 
                 input[0] = ch_input
@@ -328,6 +332,7 @@ nextflow_workflow {
 
     test("deseq2 and limma - mouse - basic") {
         config './deseq2_limmavoom_basic.config'
+        tag "deseq2+limmavoom"
 
         when {
             workflow {
@@ -439,7 +444,7 @@ nextflow_workflow {
                         file(testData.expression_test_data_dir + testData.abundance_file),
                         'propd',
                         1.5,       // FC threshold
-                        50         // weighted connectivity threshold
+                        100        // weighted connectivity threshold
                     ]
                 )
 
@@ -469,6 +474,7 @@ nextflow_workflow {
 
     test("stub") {
         config './deseq2_basic.config'
+        tag "stub"
 
         options "-stub"
 

diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap
@@ -434,9 +434,9 @@
                         "blocking": "",
                         "method": "propd",
                         "fc_threshold": 1.5,
-                        "padj_threshold": 50
+                        "padj_threshold": 100
                     },
-                    "treatment_mCherry_hND6__test_filtered.tsv:md5,67dd007d63858e49591c3de6fc77ccd6"
+                    "treatment_mCherry_hND6__test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5"
                 ],
                 [
                     {
@@ -473,9 +473,9 @@
                         "blocking": "sample_number",
                         "method": "propd",
                         "fc_threshold": 1.5,
-                        "padj_threshold": 50
+                        "padj_threshold": 100
                     },
-                    "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,67dd007d63858e49591c3de6fc77ccd6"
+                    "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5"
                 ]
             ],
             [
@@ -1095,9 +1095,9 @@
                         "blocking": "",
                         "method": "propd",
                         "fc_threshold": 1.5,
-                        "padj_threshold": 50
+                        "padj_threshold": 100
                     },
-                    "treatment_mCherry_hND6__test_filtered.tsv:md5,67dd007d63858e49591c3de6fc77ccd6"
+                    "treatment_mCherry_hND6__test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5"
                 ],
                 [
                     {
@@ -1108,9 +1108,9 @@
                         "blocking": "sample_number",
                         "method": "propd",
                         "fc_threshold": 1.5,
-                        "padj_threshold": 50
+                        "padj_threshold": 100
                     },
-                    "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,67dd007d63858e49591c3de6fc77ccd6"
+                    "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5"
                 ]
             ],
             [

diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/propd_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/propd_basic.config
@@ -2,4 +2,7 @@ process {
     withName: 'PROPR_PROPD' {
         ext.args = {"--round_digits 5 --save_adjacency true"}
     }
+    withName: 'CUSTOM_FILTERDIFFERENTIALTABLE' {
+        ext.args = {["comparison2" : ">="]}
+    }
 }