fixed trailing whitespaces

nf-core · Oct 24, 2024 · ca5e78e · ca5e78e
1 parent e5a0772
commit ca5e78e
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Showing 5 changed files with 53 additions and 53 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -10,7 +10,7 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
+    // Defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }

diff --git a/modules/local/gzrt/main.nf b/modules/local/gzrt/main.nf
@@ -12,12 +12,12 @@ process GZRT {
 
     when:
     task.ext.when == null || task.ext.when
-    
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def filename = "${fastqgz.baseName}"
-        
+
     """
     ver_line=""
     if [[ $fastqgz == *.fastq ]] || [[ $fastqgz == *.fq ]]; then
@@ -36,7 +36,7 @@ process GZRT {
 
     stub:
     def args = task.ext.args ?: ''
-    
+
     """
     ver_line=""
     if [[ $fastqgz == *.fastq ]] || [[ $fastqgz == *.fq ]]; then

diff --git a/nf-test.config b/nf-test.config
@@ -9,4 +9,4 @@ config {
     configFile "tests/nextflow.config"
 
     profile "docker"
-}
+}
diff --git a/subworkflows/local/scatter_wipe_gather/main.nf b/subworkflows/local/scatter_wipe_gather/main.nf
@@ -24,11 +24,11 @@ workflow SCATTER_WIPE_GATHER {
     ch_fastq_gather  = Channel.empty()
     ch_report_gather = Channel.empty()
     ch_fastq_gather  = WIPER.out.fixed_fastq.map{ metaData, fastq -> tuple( (fastq.baseName =~ /(.+)_chunk/)[0][1], metaData, fastq ) }
-                                     .groupTuple()
-                                     .map{ basename, metadata, fastq -> tuple(basename, metadata.first(), fastq) }
+                                    .groupTuple()
+                                    .map{ basename, metadata, fastq -> tuple(basename, metadata.first(), fastq) }
     ch_report_gather = WIPER.out.report.map{ metaData, report -> tuple( (report.baseName =~ /(.+)_chunk/)[0][1], metaData, report ) }
-                                       .groupTuple()
-                                       .map{ basename, metadata, report -> tuple(basename, metadata.first(), report) }
+                                    .groupTuple()
+                                    .map{ basename, metadata, report -> tuple(basename, metadata.first(), report) }
     GATHER(
         ch_fastq_gather,
         ch_report_gather

diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -1,44 +1,44 @@
-nextflow_pipeline {
-
-    name "Test fastqrepair pipeline"
-    script "../main.nf"
-
-    tag "pipeline"
-    tag "fastqrepair"
-    
-    test("Run fastqrepair on 30 paired-end reads with profile test") {
-
-        when {
-            params {
-                input                   = 'https://raw.githubusercontent.com/nf-core/test-datasets/fastqrepair/testdata/samplesheet_30reads.csv'
-                outdir                  = "$outputDir/30reads"
-                
-                publish_dir_all_tools   = true
-                chunk_size              = 40  // 40 lines per chunk
-
-                max_cpus                = 2
-                max_memory              = '1.GB'
-                max_time                = '1.h'
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(
-                    // path("$outputDir/30reads/wiper").list(),
-                    path("$outputDir/30reads/gather/test_30reads_R1.fastq_recovered_merged_report.txt"),
-                    path("$outputDir/30reads/gather/test_30reads_R2.fastq_recovered_merged_report.txt"),
-                    ).match("30reads_paired_end") 
-                },
-                { assert new File("$outputDir/30reads/pipeline_info/nf-core_fastqrepair_versions.yml").exists() },
-                { assert new File("$outputDir/30reads/pickup/test_30reads_R1_repaired.fastq.gz").exists() },
-                { assert new File("$outputDir/30reads/pickup/test_30reads_R2_repaired.fastq.gz").exists() },
-                { assert new File("$outputDir/30reads/gather/test_30reads_R1.fastq_recovered_merged_report.txt").readLines()[0].contains("FASTQWIPER SUMMARY:") },
-                { assert new File("$outputDir/30reads/gather/test_30reads_R1.fastq_recovered_merged_report.txt").readLines()[2].contains("68/149 (45.64%)") }
-
-                // { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }
-            )
-        }
-    }
-}
+nextflow_pipeline {
+
+    name "Test fastqrepair pipeline"
+    script "../main.nf"
+
+    tag "pipeline"
+    tag "fastqrepair"
+
+    test("Run fastqrepair on 30 paired-end reads with profile test") {
+
+        when {
+            params {
+                input                   = 'https://raw.githubusercontent.com/nf-core/test-datasets/fastqrepair/testdata/samplesheet_30reads.csv'
+                outdir                  = "$outputDir/30reads"
+
+                publish_dir_all_tools   = true
+                chunk_size              = 40  // 40 lines per chunk
+
+                max_cpus                = 2
+                max_memory              = '1.GB'
+                max_time                = '1.h'
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // path("$outputDir/30reads/wiper").list(),
+                    path("$outputDir/30reads/gather/test_30reads_R1.fastq_recovered_merged_report.txt"),
+                    path("$outputDir/30reads/gather/test_30reads_R2.fastq_recovered_merged_report.txt"),
+                    ).match("30reads_paired_end")
+                },
+                { assert new File("$outputDir/30reads/pipeline_info/nf-core_fastqrepair_versions.yml").exists() },
+                { assert new File("$outputDir/30reads/pickup/test_30reads_R1_repaired.fastq.gz").exists() },
+                { assert new File("$outputDir/30reads/pickup/test_30reads_R2_repaired.fastq.gz").exists() },
+                { assert new File("$outputDir/30reads/gather/test_30reads_R1.fastq_recovered_merged_report.txt").readLines()[0].contains("FASTQWIPER SUMMARY:") },
+                { assert new File("$outputDir/30reads/gather/test_30reads_R1.fastq_recovered_merged_report.txt").readLines()[2].contains("68/149 (45.64%)") }
+
+                // { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }
+            )
+        }
+    }
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,4 +9,4 @@ config { @@
         configFile "tests/nextflow.config"
         profile "docker"
-    }
+    }