From d134e78a0aa14fef469e30c8d90006092c9f3a6b Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Mon, 18 Nov 2024 12:29:00 -0600
Subject: [PATCH] style: Run lsp format on a parabricks module

For science
---
 modules/nf-core/parabricks/applybqsr/main.nf | 31 ++++++++++----------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/parabricks/applybqsr/main.nf b/modules/nf-core/parabricks/applybqsr/main.nf
index 38b2af002b8..0607a11d08a 100644
--- a/modules/nf-core/parabricks/applybqsr/main.nf
+++ b/modules/nf-core/parabricks/applybqsr/main.nf
@@ -1,8 +1,7 @@
 process PARABRICKS_APPLYBQSR {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
     label 'process_gpu'
-
     container "nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1"
 
     input:
@@ -15,7 +14,7 @@ process PARABRICKS_APPLYBQSR {
     output:
     tuple val(meta), path("*.bam"), emit: bam
     tuple val(meta), path("*.bai"), emit: bai
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,28 +22,28 @@ process PARABRICKS_APPLYBQSR {
     script:
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
+        error("Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead.")
     }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def interval_command = intervals ? intervals.collect{"--interval-file $it"}.join(' ') : ""
-    def copy_index_command = bam_index ? "cp -L $bam_index `readlink -f $bam`.bai" : ""
-    def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
+    def interval_command = intervals ? intervals.collect { "--interval-file ${it}" }.join(' ') : ""
+    def copy_index_command = bam_index ? "cp -L ${bam_index} `readlink -f ${bam}`.bai" : ""
+    def num_gpus = task.accelerator ? "--num-gpus ${task.accelerator.request}" : ''
     """
     # parabricks complains when index is not a regular file in the same directory as the bam
     # copy the index to this path.
-    $copy_index_command
+    ${copy_index_command}
 
     pbrun \\
         applybqsr \\
-        --ref $fasta \\
-        --in-bam $bam \\
-        --in-recal-file $bqsr_table \\
-        $interval_command \\
+        --ref ${fasta} \\
+        --in-bam ${bam} \\
+        --in-recal-file ${bqsr_table} \\
+        ${interval_command} \\
         --out-bam ${prefix}.bam \\
-        --num-threads $task.cpus \\
-        $num_gpus \\
-        $args
+        --num-threads ${task.cpus} \\
+        ${num_gpus} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -55,7 +54,7 @@ process PARABRICKS_APPLYBQSR {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def interval_command = intervals ? intervals.collect{"--interval-file $it"}.join(' ') : ""
+    def interval_command = intervals ? intervals.collect { "--interval-file ${it}" }.join(' ') : ""
     """
     touch ${prefix}.bam
     touch ${prefix}.bam.bai