Clean up module file

software/fastqc/environment.yml

@@ -6,4 +6,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - fastqc=0.11.8
+  - fastqc=0.11.9

software/fastqc/main.nf

@@ -1,37 +1,23 @@
 nextflow.preview.dsl = 2
 
 process FASTQC {
-
-    // tag "FastQC - $sample_id"
-
     input:
         tuple val(name), path(reads)
-        val (outputdir)
-        // fastqc_args are best passed into the workflow in the following manner:
-        // --fastqc_args="--nogroup -a custom_adapter_file.txt"
         val (fastqc_args)
-        val (verbose)
+        val (outputdir)
 
     output:
         tuple val(name), path ("*fastqc*"), emit: all
         path "*.zip",                       emit: report // e.g. for MultiQC later
 
-    // container 'quay.io/biocontainers/fastqc:0.11.8--2'
+    container 'quay.io/biocontainers/fastqc:0.11.8--2'
 
     publishDir "$outputdir",
         mode: "copy", overwrite: true
 
     script:
-
-        if (verbose){
-            println ("[MODULE] FASTQC ARGS: " + fastqc_args)
-        }
-
         """
-        module load fastqc
         fastqc $fastqc_args -q -t 2 $reads
-
         fastqc --version &> fastqc.version.txt
         """
-
 }