Changes in module 'nf-core/mageck/count'
--- modules/nf-core/mageck/count/main.nf
+++ modules/nf-core/mageck/count/main.nf
@@ -1,6 +1,6 @@
 process MAGECK_COUNT {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

@@ -8,13 +8,16 @@
         'biocontainers/mageck:0.5.9--py37h6bb024c_0' }"
 
     input:
-    tuple val(meta), path(inputfile)
+    tuple val(meta), path(fastq1), path(fastq2)

     path(library)
 
     output:
-    tuple val(meta), path("*count*.txt"), emit: count
+    tuple val(meta), path("*count.txt"),             emit: count
     tuple val(meta), path("*.count_normalized.txt"), emit: norm
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.countsummary.txt"),     emit: summary
+    tuple val(meta), path("*.count_normalized.txt"), emit: normalized
+    tuple val(meta), path("*.log"),                  emit: logs
+    path "versions.yml",                             emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,9 +25,15 @@

     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input_file = ("$inputfile".endsWith(".fastq.gz")) ? "--fastq ${inputfile}" : "-k ${inputfile}"
-    def sample_label = ("$inputfile".endsWith(".fastq.gz") || "$inputfile".endsWith(".fq.gz")) ? "--sample-label ${meta.id}" : ''
-
+   // def input_file = ("$inputfile".endsWith(".fastq.gz") || "$inputfile".endsWith(".fq.gz")) ? "--fastq ${inputfile}" : "-k ${inputfile}" 
+    def sample_label = ("$fastq1".endsWith(".fastq.gz") || "$fastq1".endsWith(".fq.gz")) ? "--sample-label ${meta.id}" : ''
+    
+    if (meta.single_end && ("$fastq1".endsWith(".fastq.gz") || "$fastq1".endsWith(".fq.gz"))) {
+        input = "--fastq $fastq1" 

+    } else {
+        input = "--fastq $fastq1 --fastq-2 $fastq2" 
+    }
 
     """
     mageck \\
         count \\
@@ -32,7 +41,7 @@
         -l $library \\
         -n $prefix \\
         $sample_label \\
-        $input_file \\
+        $input \\
 
 
     cat <<-END_VERSIONS > versions.yml

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