style: Touch a module that works with arm

Author: edmundmiller

modules/nf-core/bowtie2/align/main.nf

@@ -1,28 +1,28 @@
 process BOWTIE2_ALIGN {
-    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/b4/b41b403e81883126c3227fc45840015538e8e2212f13abc9ae84e4b98891d51c/data' :
-        'community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:edeb13799090a2a6' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b41b403e81883126c3227fc45840015538e8e2212f13abc9ae84e4b98891d51c/data'
+        : 'community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:edeb13799090a2a6'}"
 
     input:
-    tuple val(meta) , path(reads)
+    tuple val(meta), path(reads)
     tuple val(meta2), path(index)
     tuple val(meta3), path(fasta)
-    val   save_unaligned
-    val   sort_bam
+    val save_unaligned
+    val sort_bam
 
     output:
-    tuple val(meta), path("*.sam")      , emit: sam     , optional:true
-    tuple val(meta), path("*.bam")      , emit: bam     , optional:true
-    tuple val(meta), path("*.cram")     , emit: cram    , optional:true
-    tuple val(meta), path("*.csi")      , emit: csi     , optional:true
-    tuple val(meta), path("*.crai")     , emit: crai    , optional:true
-    tuple val(meta), path("*.log")      , emit: log
-    tuple val(meta), path("*fastq.gz")  , emit: fastq   , optional:true
-    path  "versions.yml"                , emit: versions
+    tuple val(meta), path("*.sam"), emit: sam, optional: true
+    tuple val(meta), path("*.bam"), emit: bam, optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.csi"), emit: csi, optional: true
+    tuple val(meta), path("*.crai"), emit: crai, optional: true
+    tuple val(meta), path("*.log"), emit: log
+    tuple val(meta), path("*fastq.gz"), emit: fastq, optional: true
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -37,17 +37,20 @@ process BOWTIE2_ALIGN {
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
         reads_args = "-U ${reads}"
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
         reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
     }
 
     def samtools_command = sort_bam ? 'sort' : 'view'
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
-    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension_matcher = (args2 =~ extension_pattern)
     def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
-    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+    def reference = fasta && extension == "cram" ? "--reference ${fasta}" : ""
+    if (!fasta && extension == "cram") {
+        error("Fasta reference is required for CRAM output")
+    }
 
     """
     INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
@@ -56,12 +59,12 @@ process BOWTIE2_ALIGN {
 
     bowtie2 \\
         -x \$INDEX \\
-        $reads_args \\
-        --threads $task.cpus \\
-        $unaligned \\
-        $args \\
+        ${reads_args} \\
+        --threads ${task.cpus} \\
+        ${unaligned} \\
+        ${args} \\
         2>| >(tee ${prefix}.bowtie2.log >&2) \\
-        | samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} -
+        | samtools ${samtools_command} ${args2} --threads ${task.cpus} ${reference} -o ${prefix}.${extension} -
 
     if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
         mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
@@ -83,19 +86,23 @@ process BOWTIE2_ALIGN {
     def args2 = task.ext.args2 ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
-    def extension = (args2 ==~ extension_pattern) ? (args2 =~ extension_pattern)[0][2].toLowerCase() : "bam"
+    def extension = args2 ==~ extension_pattern ? (args2 =~ extension_pattern)[0][2].toLowerCase() : "bam"
     def create_unmapped = ""
     if (meta.single_end) {
         create_unmapped = save_unaligned ? "touch ${prefix}.unmapped.fastq.gz" : ""
-    } else {
+    }
+    else {
         create_unmapped = save_unaligned ? "touch ${prefix}.unmapped_1.fastq.gz && touch ${prefix}.unmapped_2.fastq.gz" : ""
     }
-    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+    if (!fasta && extension == "cram") {
+        error("Fasta reference is required for CRAM output")
+    }
 
     def create_index = ""
     if (extension == "cram") {
         create_index = "touch ${prefix}.crai"
-    } else if (extension == "bam") {
+    }
+    else if (extension == "bam") {
         create_index = "touch ${prefix}.csi"
     }
 
@@ -112,5 +119,4 @@ process BOWTIE2_ALIGN {
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
-
 }