Fix linting

nf-core · Apr 20, 2024 · 914eafd · 914eafd
1 parent a806201
commit 914eafd
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/modules/local/fishpond/swish/main.nf b/modules/local/fishpond/swish/main.nf
@@ -27,4 +27,4 @@ process FISHPOND_SWISH {
         bioconductor-fishpond: \$(Rscript -e "library(fishpond); cat(as.character(packageVersion('fishpond')))")
     END_VERSIONS
     """
-}
+}
diff --git a/modules/local/fishpond/swish/templates/swish.r b/modules/local/fishpond/swish/templates/swish.r
@@ -11,18 +11,18 @@ phenotype <- read.csv('${phenotype}', stringsAsFactors = FALSE)
 se_assays <- list()
 
 for (se in experiments) {
-  assays <- assays(se)
-  # Iterate over named list of assays
-  for (assay_name in names(assays)) {
-    assay <- assays[[assay_name]]
-
-    # Add assay to se_assays for its name
-    if (is.null(se_assays[[assay_name]])) {
-      se_assays[[assay_name]] <- assay
-    } else {
-      se_assays[[assay_name]] <- cbind(se_assays[[assay_name]], assay)
+    assays <- assays(se)
+    # Iterate over named list of assays
+    for (assay_name in names(assays)) {
+        assay <- assays[[assay_name]]
+
+        # Add assay to se_assays for its name
+        if (is.null(se_assays[[assay_name]])) {
+            se_assays[[assay_name]] <- assay
+        } else {
+            se_assays[[assay_name]] <- cbind(se_assays[[assay_name]], assay)
+        }
     }
-  }
 }
 
 se_cbind <- do.call(SummarizedExperiment::cbind, experiments)
@@ -43,4 +43,4 @@ writeLines(
         '"${task.process}":',
         paste('    bioconductor-fishpond:', packageVersion('fishpond'))
     ),
-'versions.yml')
+'versions.yml')
diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf
@@ -120,5 +120,5 @@ workflow QUANTIFICATION {
     circular_tx_counts = SPLIT_TYPES_COUNTS.out.circular
     circular_tx_tpm    = SPLIT_TYPES_TPM.out.circular
 
-    versions        = ch_versions
+    versions           = ch_versions
 }