Revert "style: Run lsp on fastqc"

This reverts commit da64fce.
nf-core · Nov 21, 2024 · f2217ca · f2217ca
1 parent afa0268
commit f2217ca
Showing 1 changed file with 14 additions and 14 deletions.
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
@@ -1,19 +1,19 @@
 process FASTQC {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0'
-        : 'biocontainers/fastqc:0.12.1--hdfd78af_0'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
+        'biocontainers/fastqc:0.12.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
 
     output:
     tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip"), emit: zip
-    path "versions.yml", emit: versions
+    tuple val(meta), path("*.zip") , emit: zip
+    path  "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,9 +22,9 @@ process FASTQC {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     // Make list of old name and new name pairs to use for renaming in the bash while loop
-    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[reads, "${prefix}.${reads.extension}"]] : reads.withIndex().collect { entry, index -> [entry, "${prefix}_${index + 1}.${entry.extension}"] }
-    def rename_to = old_new_pairs.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect { old_name, new_name -> new_name }.join(' ')
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
@@ -34,15 +34,15 @@ process FASTQC {
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
     """
-    printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
 
     fastqc \\
-        ${args} \\
-        --threads ${task.cpus} \\
-        --memory ${fastqc_memory} \\
-        ${renamed_files}
+        $args \\
+        --threads $task.cpus \\
+        --memory $fastqc_memory \\
+        $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":