style: Run lsp format

nf-core · Dec 6, 2024 · 786b4f8 · 786b4f8
1 parent 3a9045a
commit 786b4f8
Showing 1 changed file with 26 additions and 18 deletions.
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
@@ -1,22 +1,22 @@
 process TRIMGALORE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9becad054093ad4083a961d12733f2a742e11728fe9aa815d678b882b3ede520/data' :
-        'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9becad054093ad4083a961d12733f2a742e11728fe9aa815d678b882b3ede520/data'
+        : 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d'}"
 
     input:
     tuple val(meta), path(reads)
 
     output:
     tuple val(meta), path("*{3prime,5prime,trimmed,val}*.fq.gz"), emit: reads
-    tuple val(meta), path("*report.txt")                        , emit: log     , optional: true
-    tuple val(meta), path("*unpaired*.fq.gz")                   , emit: unpaired, optional: true
-    tuple val(meta), path("*.html")                             , emit: html    , optional: true
-    tuple val(meta), path("*.zip")                              , emit: zip     , optional: true
-    path "versions.yml"                                         , emit: versions
+    tuple val(meta), path("*report.txt"), emit: log, optional: true
+    tuple val(meta), path("*unpaired*.fq.gz"), emit: unpaired, optional: true
+    tuple val(meta), path("*.html"), emit: html, optional: true
+    tuple val(meta), path("*.zip"), emit: zip, optional: true
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,9 +29,15 @@ process TRIMGALORE {
     def cores = 1
     if (task.cpus) {
         cores = (task.cpus as int) - 4
-        if (meta.single_end) cores = (task.cpus as int) - 3
-        if (cores < 1) cores = 1
-        if (cores > 8) cores = 8
+        if (meta.single_end) {
+            cores = (task.cpus as int) - 3
+        }
+        if (cores < 1) {
+            cores = 1
+        }
+        if (cores > 8) {
+            cores = 8
+        }
     }
 
     // Added soft-links to original fastqs for consistent naming in MultiQC
@@ -40,10 +46,10 @@ process TRIMGALORE {
         def args_list = args.split("\\s(?=--)").toList()
         args_list.removeAll { it.toLowerCase().contains('_r2 ') }
         """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        [ ! -f  ${prefix}.fastq.gz ] && ln -s ${reads} ${prefix}.fastq.gz
         trim_galore \\
             ${args_list.join(' ')} \\
-            --cores $cores \\
+            --cores ${cores} \\
             --gzip \\
             ${prefix}.fastq.gz
 
@@ -53,13 +59,14 @@ process TRIMGALORE {
             cutadapt: \$(cutadapt --version)
         END_VERSIONS
         """
-    } else {
+    }
+    else {
         """
         [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
         [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
         trim_galore \\
-            $args \\
-            --cores $cores \\
+            ${args} \\
+            --cores ${cores} \\
             --paired \\
             --gzip \\
             ${prefix}_1.fastq.gz \\
@@ -78,7 +85,8 @@ process TRIMGALORE {
     if (meta.single_end) {
         output_command = "echo '' | gzip > ${prefix}_trimmed.fq.gz ;"
         output_command += "touch ${prefix}.fastq.gz_trimming_report.txt"
-    } else {
+    }
+    else {
         output_command = "echo '' | gzip > ${prefix}_1_trimmed.fq.gz ;"
         output_command += "touch ${prefix}_1.fastq.gz_trimming_report.txt ;"
         output_command += "echo '' | gzip > ${prefix}_2_trimmed.fq.gz ;"