Fix linting and include propd_grea in test

nf-core · Oct 22, 2024 · 1cbdb17 · 1cbdb17
1 parent 41adc93
commit 1cbdb17
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/conf/test_experimental.config b/conf/test_experimental.config
@@ -30,7 +30,7 @@ params {
     matrix =  'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
     contrasts =  'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv'
     tools = "$projectDir/assets/tools_samplesheet.csv"
-    pathway = "propd,propd_fdr,pcorbshrink,propr,cor"
+    pathway = "propd,propd_fdr,pcorbshrink,propr,cor,propd_grea"
 
     //Features
     features_metadata_cols      = 'gene_id,gene_name'

diff --git a/subworkflows/local/correlation/main.nf b/subworkflows/local/correlation/main.nf
@@ -3,7 +3,7 @@
 //
 include {PROPR_PROPR as PROPR} from "../../../modules/local/propr/propr/main.nf"
 
-def clean_meta = { meta, data -> 
+def clean_meta = { meta, data ->
     def meta_clone = meta.clone()
     meta_clone.remove('cor_method')
     meta_clone.remove('args_cor')

diff --git a/subworkflows/local/differential/main.nf b/subworkflows/local/differential/main.nf
@@ -4,7 +4,7 @@
 include { PROPR_PROPD as PROPD } from "../../../modules/local/propr/propd/main.nf"
 include { DESEQ2_DIFFERENTIAL  } from '../../../modules/nf-core/deseq2/differential/main'
 
-def clean_meta = { meta, data -> 
+def clean_meta = { meta, data ->
     def meta_clone = meta.clone()
     meta_clone.remove('diff_method')
     meta_clone.remove('args_diff')

diff --git a/subworkflows/local/enrichment/main.nf b/subworkflows/local/enrichment/main.nf
@@ -34,8 +34,8 @@ workflow ENRICHMENT {
     ch_adjacency
         .map { meta, matrix -> [meta.subMap(["pathway_name"]), meta, matrix] }
         .join(ch_tools, by: [0])
-        .map { 
-            pathway_name, meta, matrix, meta_tools -> 
+        .map {
+            pathway_name, meta, matrix, meta_tools ->
                 def new_meta = meta.clone() + meta_tools.clone()
                 [ new_meta, matrix ]
             }