Tidy up configs

nf-core · Dec 7, 2024 · 7ef3d17 · 7ef3d17
1 parent ec0f45f
commit 7ef3d17
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Showing 5 changed files with 24 additions and 22 deletions.
diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_basic.config
@@ -3,4 +3,8 @@ process {
         ext.args = { "--round_digits 5 --blocking_variables $meta.blocking --vs_method rlog" }
         ext.prefix = { "${meta.id}_${meta.method}" }
     }
+
+    withName: 'DESEQ2_NORM' {
+        ext.prefix = { "${meta.id}_${meta.method}_voom_norm" }
+    }
 }
diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_basic.config
@@ -4,6 +4,10 @@ process {
         ext.prefix = { "${meta.id}_${meta.method}" }
     }
 
+    withName: 'DESEQ2_NORM' {
+        ext.prefix = { "${meta.id}_${meta.method}_voom_norm" }
+    }
+
     withName: 'LIMMA_DIFFERENTIAL' {
         ext.args = { [
             "--sample_id_col sample",
@@ -14,11 +18,6 @@ process {
     }
 
     withName: 'LIMMA_NORM' {
-        ext.args = { [
-            "--sample_id_col sample",
-            "--probe_id_col gene_id",
-            "--use_voom TRUE"
-        ].join(' ').trim() }
         ext.prefix = { "${meta.id}_${meta.method}_voom_norm" }
     }
 }
diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/limma_basic_microarray.config b/subworkflows/nf-core/abundance_differential_filter/tests/limma_basic_microarray.config
@@ -8,6 +8,10 @@ process {
         ext.prefix = { "${meta.id}_${meta.method}" }
     }
 
+    withName: 'LIMMA_NORM' {
+        ext.prefix = { "${meta.id}_${meta.method}_norm" }
+    }
+
     withName: 'AFFY_JUSTRMA' {
         ext.args = "--sample_name_col name"
         publishDir = [ enabled: false ]

diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/limma_voom.config b/subworkflows/nf-core/abundance_differential_filter/tests/limma_voom.config
@@ -11,11 +11,6 @@ process {
     }
 
     withName: 'LIMMA_NORM' {
-        ext.args = { [
-            "--sample_id_col sample",
-            "--probe_id_col gene_id",
-            "--use_voom TRUE"
-        ].join(' ').trim() }
         ext.prefix = { "${meta.id}_${meta.method}_voom_norm" }
     }
 }
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
@@ -50,7 +50,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-06T18:44:02.534049083"
+        "timestamp": "2024-12-07T14:13:58.444319315"
     },
     "deseq2 and limma - mouse - basic": {
         "content": [
@@ -140,7 +140,7 @@
                         "blocking": "",
                         "method": "deseq2"
                     },
-                    "treatment_mCherry_hND6__test_deseq2.normalised_counts.tsv:md5,46ab7200c626649ab6256ed797ef5071"
+                    "treatment_mCherry_hND6__test_deseq2_voom_norm.normalised_counts.tsv:md5,46ab7200c626649ab6256ed797ef5071"
                 ],
                 [
                     {
@@ -175,7 +175,7 @@
                         "blocking": "",
                         "method": "deseq2"
                     },
-                    "treatment_mCherry_hND6__test_deseq2.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030"
+                    "treatment_mCherry_hND6__test_deseq2_voom_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030"
                 ]
             ],
             [
@@ -223,7 +223,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-06T18:45:42.91334032"
+        "timestamp": "2024-12-07T14:15:50.472973281"
     },
     "limma - voom": {
         "content": [
@@ -312,7 +312,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-06T18:44:20.316709196"
+        "timestamp": "2024-12-07T14:14:35.356602483"
     },
     "stub": {
         "content": [
@@ -463,7 +463,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-06T18:46:01.912198249"
+        "timestamp": "2024-12-07T14:16:11.269323961"
     },
     "deseq2 - mouse - basic": {
         "content": [
@@ -505,7 +505,7 @@
                         "blocking": "",
                         "method": "deseq2"
                     },
-                    "treatment_mCherry_hND6__test_deseq2.normalised_counts.tsv:md5,46ab7200c626649ab6256ed797ef5071"
+                    "treatment_mCherry_hND6__test_deseq2_voom_norm.normalised_counts.tsv:md5,46ab7200c626649ab6256ed797ef5071"
                 ]
             ],
             [
@@ -518,7 +518,7 @@
                         "blocking": "",
                         "method": "deseq2"
                     },
-                    "treatment_mCherry_hND6__test_deseq2.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030"
+                    "treatment_mCherry_hND6__test_deseq2_voom_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030"
                 ]
             ],
             [
@@ -542,7 +542,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-06T18:43:19.657748379"
+        "timestamp": "2024-12-07T14:12:59.70075456"
     },
     "deseq2 - with transcript lengths": {
         "content": [
@@ -584,7 +584,7 @@
                         "blocking": "",
                         "method": "deseq2"
                     },
-                    "treatment_mCherry_hND6__test_deseq2.normalised_counts.tsv:md5,7050f44c460cc13e3f101d048d503527"
+                    "treatment_mCherry_hND6__test_deseq2_voom_norm.normalised_counts.tsv:md5,7050f44c460cc13e3f101d048d503527"
                 ]
             ],
             [
@@ -597,7 +597,7 @@
                         "blocking": "",
                         "method": "deseq2"
                     },
-                    "treatment_mCherry_hND6__test_deseq2.rlog.tsv:md5,22a4b117246b2317e0f4daf7919703f2"
+                    "treatment_mCherry_hND6__test_deseq2_voom_norm.rlog.tsv:md5,22a4b117246b2317e0f4daf7919703f2"
                 ]
             ],
             [
@@ -621,6 +621,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-06T18:45:00.361148507"
+        "timestamp": "2024-12-07T14:15:12.184775725"
     }
 }