From 57ab6dbcbf6e891c08133130c337cade188aefd8 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Thu, 17 Dec 2020 10:24:48 +0100
Subject: [PATCH] groovy formatting

---
 software/bowtie/align/main.nf | 18 +++++++++---------
 software/bowtie/index/main.nf | 12 ++++++------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf
index 58906d61..4271d33a 100644
--- a/software/bowtie/align/main.nf
+++ b/software/bowtie/align/main.nf
@@ -11,21 +11,21 @@ process BOWTIE_ALIGN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.10' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+        container 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
     } else {
-        container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
+        container 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
     }
 
     input:
     tuple val(meta), path(reads)
     path  index
-    
+
     output:
-    tuple val(meta), path("*.bam"), emit: bam
-    tuple val(meta), path("*.out"), emit: log
-    path  "bowtie.version.txt", emit: version
+    tuple val(meta), path('*.bam'), emit: bam
+    tuple val(meta), path('*.out'), emit: log
+    path  'bowtie.version.txt', emit: version
 
     script:
     def software  = getSoftwareName(task.process)
@@ -39,10 +39,10 @@ process BOWTIE_ALIGN {
         --sam \\
         -x \$INDEX \\
         -q \\
-	    $unaligned \\
+        $unaligned \\
         $options.args \\
         $endedness \\
-	    2> ${prefix}.out \\
+        2> ${prefix}.out \\
         | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
diff --git a/software/bowtie/index/main.nf b/software/bowtie/index/main.nf
index 1a3801b6..38f1c289 100644
--- a/software/bowtie/index/main.nf
+++ b/software/bowtie/index/main.nf
@@ -11,19 +11,19 @@ process BOWTIE_INDEX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    conda (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
+    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1"
+        container 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1'
     } else {
-        container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
+        container 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1'
     }
 
     input:
     path fasta
 
     output:
-    path "bowtie", emit: index
-    path "*.version.txt", emit: version
+    path 'bowtie', emit: index
+    path '*.version.txt', emit: version
 
     script:
     def software  = getSoftwareName(task.process)
@@ -32,4 +32,4 @@ process BOWTIE_INDEX {
     bowtie-build --threads $task.cpus ${fasta} bowtie/${fasta.baseName}.index
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
     """
-}
\ No newline at end of file
+}