Fixing EditorConfig linting failures

nf-core · Oct 4, 2023 · caea67c · caea67c
1 parent 3e4a923
commit caea67c
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Showing 9 changed files with 40 additions and 255 deletions.
diff --git a/bin/merge_counts.R b/bin/merge_counts.R
@@ -62,7 +62,7 @@ message("--- Remove the columns ---")
 shared_column_table <- merged_table %>% select(ends_with(".x") | ends_with(".y"))
 unshared_column_table <- merged_table %>% select(!(ends_with(".x") | ends_with(".y")))
 
-# We only want to look at merged 
+# We only want to look at merged
 bc_prefixes <- unique(sub("\\..*", "", colnames(shared_column_table)))
 
 # Do rowsums for columns that are the same barcode
@@ -87,4 +87,5 @@ sessioninfo <- "R_sessionInfo.log"
 
 sink(sessioninfo)
 sessionInfo()
-sink()
+sink()
+
diff --git a/bin/seurat_qc.R b/bin/seurat_qc.R
@@ -22,33 +22,33 @@ library(ggplot2)
 #' @return A density plot
 
 plotSingleCellDensity <- function(input_obj,
-                                  metadata_variable,
-                                  group.by = "orig.ident",
-                                  scale_x_axis = FALSE,
-                                  geom_density_level = 0.2) {
-
-  metadata <- dplyr::select(
-    input_obj@meta.data,
-    {{ metadata_variable }},
-    {{ group.by }}
-  )
-
-  meta_density <- ggplot2::ggplot(
-    metadata,
-    aes(
-      x = .data[[metadata_variable]],
-      color = .data[[group.by]],
-      fill = .data[[group.by]]
+                                    metadata_variable,
+                                    group.by = "orig.ident",
+                                    scale_x_axis = FALSE,
+                                    geom_density_level = 0.2) {
+
+    metadata <- dplyr::select(
+        input_obj@meta.data,
+        {{ metadata_variable }},
+        {{ group.by }}
     )
-  ) +
+
+    meta_density <- ggplot2::ggplot(
+        metadata,
+        aes(
+            x = .data[[metadata_variable]],
+            color = .data[[group.by]],
+            fill = .data[[group.by]]
+        )
+    ) +
     geom_density(alpha = geom_density_level) +
     theme_classic()
 
-  if (scale_x_axis == TRUE) {
-    return(meta_density + scale_x_log10())
-  } else {
-    return(meta_density)
-  }
+    if (scale_x_axis == TRUE) {
+        return(meta_density + scale_x_log10())
+    } else {
+        return(meta_density)
+    }
 }
 
 ###############################
@@ -102,9 +102,9 @@ total_reads <- as.numeric(gsub("([0-9]+).*$", "\\1", flagstat_lines[index_nums])
 # Create the Seurat object
 #NOTE: we do not perform any pre-filtering at this point
 seurat_obj <- CreateSeuratObject(counts = cell_bc_matrix,
-                                 min.cells = 0,
-                                 min.features = 0,
-                                 project = opt$id)
+                                    min.cells = 0,
+                                    min.features = 0,
+                                    project = opt$id)
 
 ######################
 ### GENERATE PLOTS ###

diff --git a/conf/modules.config b/conf/modules.config
@@ -144,7 +144,7 @@ if (!params.skip_qc){
             ]
         }
     }
-    
+
     process {
         withName:'.*:BAM_SORT_STATS_SAMTOOLS_FILTERED:BAM_STATS_SAMTOOLS:.*' {
             ext.prefix = { "${meta.id}.mapped_only" }
@@ -155,7 +155,7 @@ if (!params.skip_qc){
             ]
         }
     }
-    
+
     process {
         withName:'.*:BAM_SORT_STATS_SAMTOOLS_CORRECTED:BAM_STATS_SAMTOOLS:.*' {
             ext.prefix = { "${meta.id}.corrected" }
@@ -166,7 +166,7 @@ if (!params.skip_qc){
             ]
         }
     }
-    
+
     process {
         withName:'.*:BAM_SORT_STATS_SAMTOOLS_DEDUP:BAM_STATS_SAMTOOLS:.*' {
             ext.prefix = { "${meta.id}.dedup" }
@@ -209,7 +209,6 @@ process {
             path: { "${params.outdir}/references/paftools" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-
         ]
     }
 }

diff --git a/module_diffs.txt b/module_diffs.txt
diff --git a/modules/local/create_regex.nf b/modules/local/create_regex.nf
@@ -5,7 +5,7 @@ process CREATE_REGEX {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3':
         'biocontainers/python:3.8.3' }"
-    
+
     input:
     val cell_barcode_pattern
     val identifier_pattern
@@ -22,13 +22,13 @@ process CREATE_REGEX {
 
     script:
     def args = task.ext.args ?: ''
-    
+
     """
     OUT_FILE="regex_patterns.txt"
 
     if [[ "${cell_barcode_pattern}" ]]; then
-       echo -e "REGEX: ${cell_barcode_pattern}" > \${OUT_FILE}
-       echo -e "UMI_TOOLS: N/A" >> \${OUT_FILE}
+        echo -e "REGEX: ${cell_barcode_pattern}" > \${OUT_FILE}
+        echo -e "UMI_TOOLS: N/A" >> \${OUT_FILE}
 
     else
         create_regex.py -i "${identifier_pattern}" \\

diff --git a/modules/local/isoquant.nf b/modules/local/isoquant.nf
@@ -66,6 +66,6 @@ process ISOQUANT {
             isoquant: \$(isoquant.py -v 2>&1)
         END_VERSIONS
         """
-    
+
     }
 }
diff --git a/modules/local/nanofilt.nf b/modules/local/nanofilt.nf
@@ -27,7 +27,7 @@ process NANOFILT {
         IDX=\$(basename ${reads} | cut -f2 -d'.')
         FILE_PREFIX=\${FILE_PREFIX}.\${IDX}
     fi
-    cat $reads | NanoFilt $args > \${FILE_PREFIX}.filtered.fastq    
+    cat $reads | NanoFilt $args > \${FILE_PREFIX}.filtered.fastq
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/prowlertrimmer.nf b/modules/local/prowlertrimmer.nf
@@ -17,7 +17,7 @@ process PROWLERTRIMMER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    
+
     """
     FILE_PREFIX=${prefix}
     if [ ${params.split_amount} -gt 0 ]; then

diff --git a/modules/local/reformat_whitelist.nf b/modules/local/reformat_whitelist.nf
@@ -21,7 +21,7 @@ process REFORMAT_WHITELIST {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    
+
     """
     reformat_whitelist.py \\
         -i ${whitelist} \\