Remove unused module and fix module structure for samplesheet_check

modules/local/ensure_fastq_extension.nf

@@ -1,31 +0,0 @@
-process ENSURE_FASTQ_EXTENSION {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda "conda-forge::bash=5.0
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
-        'biocontainers/biocontainers:v1.2.0_cv2' }"
-
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path('*.fastq.gz'), emit: reads
-
-    script:
-    if (meta.single_end) {
-        fastq = "${reads.baseName}.fastq.gz"
-        """
-        ln -s '${reads}' '${fastq}'
-        """
-    } else {
-        first = "${reads[0].baseName}.fastq.gz"
-        second = "${reads[1].baseName}.fastq.gz"
-        """
-        ln -s '${reads[0]}' '${first}'
-        ln -s '${reads[1]}' '${second}'
-        """
-    }
-}

modules/local/samplesheet_check.nf

@@ -1,5 +1,6 @@
 process SAMPLESHEET_CHECK {
     tag "$samplesheet"
+    label 'process_single'
 
     conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -13,6 +14,9 @@ process SAMPLESHEET_CHECK {
     path '*.csv'       , emit: csv
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
     """
     check_samplesheet.py \\