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nf-core · Dec 20, 2024 · ae39a00 · ae39a00
1 parent 5cc6fd0
commit ae39a00
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Showing 4 changed files with 18 additions and 18 deletions.
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
@@ -3,6 +3,9 @@
         "content": [
             21,
             {
+                "CUSTOM_TABULARTOGSEACHIP": {
+                    "gawk": "5.1.0"
+                },
                 "DESEQ2_DIFFERENTIAL": {
                     "r-base": "4.1.3",
                     "bioconductor-deseq2": "1.34.0"
@@ -23,9 +26,6 @@
                 "PLOT_EXPLORATORY": {
                     "r-shinyngs": "2.0.0"
                 },
-                "TABULAR_TO_GSEA_CHIP": {
-                    "bash": "5.2.21 3"
-                },
                 "VALIDATOR": {
                     "r-base": "4.3.3",
                     "r-shinyngs": "2.0.0"
@@ -186,12 +186,15 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T11:56:20.743162854"
+        "timestamp": "2024-12-20T16:13:56.445211657"
     },
     "Test profile with yaml contrasts": {
         "content": [
             21,
             {
+                "CUSTOM_TABULARTOGSEACHIP": {
+                    "gawk": "5.1.0"
+                },
                 "DESEQ2_DIFFERENTIAL": {
                     "r-base": "4.1.3",
                     "bioconductor-deseq2": "1.34.0"
@@ -212,9 +215,6 @@
                 "PLOT_EXPLORATORY": {
                     "r-shinyngs": "2.0.0"
                 },
-                "TABULAR_TO_GSEA_CHIP": {
-                    "bash": "5.2.21 3"
-                },
                 "VALIDATOR": {
                     "r-base": "4.3.3",
                     "r-shinyngs": "2.0.0"
@@ -375,6 +375,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-20T13:41:10.4647836"
+        "timestamp": "2024-12-20T16:16:49.167979669"
     }
 }
diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap
@@ -7,6 +7,9 @@
                     "r-base": "4.3.1",
                     "bioconductor-affy": "1.78.0"
                 },
+                "CUSTOM_TABULARTOGSEACHIP": {
+                    "gawk": "5.1.0"
+                },
                 "GSEA_GSEA": {
                     "gsea": "4.3.2"
                 },
@@ -21,9 +24,6 @@
                 "PLOT_EXPLORATORY": {
                     "r-shinyngs": "2.0.0"
                 },
-                "TABULAR_TO_GSEA_CHIP": {
-                    "bash": "5.2.21 3"
-                },
                 "VALIDATOR": {
                     "r-base": "4.3.3",
                     "r-shinyngs": "2.0.0"
@@ -236,6 +236,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T12:03:13.731672183"
+        "timestamp": "2024-12-20T15:43:35.560675645"
     }
 }
diff --git a/tests/test_rnaseq_limma.nf.test.snap b/tests/test_rnaseq_limma.nf.test.snap
@@ -3,6 +3,9 @@
         "content": [
             20,
             {
+                "CUSTOM_TABULARTOGSEACHIP": {
+                    "gawk": "5.1.0"
+                },
                 "GSEA_GSEA": {
                     "gsea": "4.3.2"
                 },
@@ -23,9 +26,6 @@
                 "PLOT_EXPLORATORY": {
                     "r-shinyngs": "2.0.0"
                 },
-                "TABULAR_TO_GSEA_CHIP": {
-                    "bash": "5.2.21 3"
-                },
                 "VALIDATOR": {
                     "r-base": "4.3.3",
                     "r-shinyngs": "2.0.0"
@@ -177,6 +177,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T12:10:44.503110769"
+        "timestamp": "2024-12-20T16:29:49.698674022"
     }
 }
diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf
@@ -465,7 +465,7 @@ workflow DIFFERENTIALABUNDANCE {
         CUSTOM_TABULARTOGSEACLS(ch_contrasts_and_samples)
 
         CUSTOM_TABULARTOGSEACHIP(
-            VALIDATOR.out.feature_meta.map{ it[1] },
+            VALIDATOR.out.feature_meta,
             [params.features_id_col, params.features_name_col]
         )
 
@@ -482,7 +482,7 @@ workflow DIFFERENTIALABUNDANCE {
         GSEA_GSEA(
             ch_gsea_inputs,
             ch_gsea_inputs.map{ tuple(it[0].reference, it[0].target) }, // *
-            CUSTOM_TABULARTOGSEACHIP.out.chip.first()
+            CUSTOM_TABULARTOGSEACHIP.out.chip.first().map{ it[1] }
         )
 
         // * Note: GSEA module currently uses a value channel for the mandatory