Whitespace

Author: chris-cheshire

subworkflows/local/align_bowtie2.nf

@@ -45,7 +45,7 @@ workflow ALIGN_BOWTIE2 {
     /*
      * Sort, index BAM file and run samtools stats, flagstat and idxstats
      */
-    BAM_SORT_STATS_SAMTOOLS ( BOWTIE2_TARGET_ALIGN.out.aligned, fasta ) 
+    BAM_SORT_STATS_SAMTOOLS ( BOWTIE2_TARGET_ALIGN.out.aligned, fasta )
     ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
 
     BAM_SORT_STATS_SAMTOOLS_SPIKEIN ( BOWTIE2_SPIKEIN_ALIGN.out.aligned, spikein_fasta )
@@ -54,7 +54,7 @@ workflow ALIGN_BOWTIE2 {
     emit:
     versions             = ch_versions                                  // channel: [ versions.yml ]
 
-    orig_bam             = BOWTIE2_TARGET_ALIGN.out.aligned             // channel: [ val(meta), bam ] 
+    orig_bam             = BOWTIE2_TARGET_ALIGN.out.aligned             // channel: [ val(meta), bam ]
     orig_spikein_bam     = BOWTIE2_SPIKEIN_ALIGN.out.aligned            // channel: [ val(meta), bam ]
 
     bowtie2_log          = BOWTIE2_TARGET_ALIGN.out.log                 // channel: [ val(meta), log_final ]

subworkflows/local/deduplicate_linear.nf

@@ -101,7 +101,7 @@ workflow DEDUPLICATE_LINEAR {
         ch_metrics           = FIND_UNIQUE_READS.out.metrics
         ch_versions          = ch_versions.mix( FIND_UNIQUE_READS.out.versions )
 
-         // Subset original .bam file to contain only unique alignments
+        // Subset original .bam file to contain only unique alignments
         ch_split.control
         .join( bai )
         .join( ch_linear_duplicates )

subworkflows/local/extract_fragments.nf

@@ -34,7 +34,7 @@ workflow EXTRACT_FRAGMENTS {
     * MODULE: Keep the read pairs that are on the same chromosome and fragment length less than 1000bp.
     */
     AWK (
-        BEDTOOLS_BAMTOBED.out.bed  
+        BEDTOOLS_BAMTOBED.out.bed
     )
     ch_versions = ch_versions.mix(AWK.out.versions)
 

subworkflows/local/extract_metadata_awk.nf

@@ -1,5 +1,5 @@
 /*
- * Generate table-based metadata from a summary report using AWK 
+ * Generate table-based metadata from a summary report using AWK
  */
 
 include { AWK_SCRIPT } from '../../modules/local/linux/awk_script'

subworkflows/local/peak_qc.nf

@@ -36,7 +36,6 @@ workflow PEAK_QC {
     .join ( flagstat.map { row -> [row[0].id, row ].flatten()} )
     .map { row -> [ row[1], row[2], row[4], row[6] ]}
     .set { ch_frip }
-    //ch_frip | view 
 
     /*
     * MODULE: Calculate frip scores for primary peaks
@@ -47,7 +46,7 @@ workflow PEAK_QC {
         min_frip_overlap
     )
     ch_versions = ch_versions.mix(PEAK_FRIP.out.versions)
-    // PEAK_FRIP.out.frip_mqc | view 
+    // PEAK_FRIP.out.frip_mqc | view
 
     /*
     * MODULE: Calculate peak counts for primary peaks
@@ -144,8 +143,8 @@ workflow PEAK_QC {
     /*
     * MODULE: Plot upset plots for sample peaks
     */
-    PLOT_CONSENSUS_PEAKS ( 
-        ch_merged_bed_sorted.ifEmpty([]) 
+    PLOT_CONSENSUS_PEAKS (
+        ch_merged_bed_sorted.ifEmpty([])
     )
     ch_versions = ch_versions.mix(PLOT_CONSENSUS_PEAKS.out.versions)
 

subworkflows/local/prepare_genome.nf

@@ -116,7 +116,7 @@ workflow PREPARE_GENOME {
     /*
     * Index genome fasta file
     */
-    ch_fasta_index = SAMTOOLS_FAIDX ( ch_fasta, [[id:"fasta"], []] ).fai  
+    ch_fasta_index = SAMTOOLS_FAIDX ( ch_fasta, [[id:"fasta"], []] ).fai
     ch_versions    = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
 
     /*

tests/config/nextflow.config

@@ -5,9 +5,9 @@ params {
 }
 
 process {
-  cpus = 2
-  memory = 6.GB
-  time = 6.h
+    cpus = 2
+    memory = 6.GB
+    time = 6.h
 }
 
 if ("$PROFILE" == "singularity") {

workflows/cutandrun.nf

@@ -358,7 +358,7 @@ workflow CUTANDRUN {
             ch_samtools_bam,
             ch_samtools_bai,
             true,
-            PREPARE_GENOME.out.fasta.collect(), 
+            PREPARE_GENOME.out.fasta.collect(),
             PREPARE_GENOME.out.fasta_index.collect()
         )
         ch_samtools_bam           = MARK_DUPLICATES_PICARD.out.bam