This should do :-)

Author: apeltzer

main.nf

@@ -148,6 +148,7 @@ params.email = false
 params.plaintext_email = false
 
 // Skipping parts of the pipeline for impatient users
+params.skip_fastqc = false 
 params.skip_adapterremoval = false
 params.skip_preseq = false
 params.skip_damage_calculation = false
@@ -532,6 +533,8 @@ process fastqc {
     publishDir "${params.outdir}/FastQC", mode: 'copy',
         saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
 
+    when: !params.skip_fastqc
+
     input:
     set val(name), file(reads) from ch_read_files_fastqc.mix(ch_read_files_converted_fastqc)
 
@@ -650,7 +653,7 @@ process fastqc_after_clipping {
     publishDir "${params.outdir}/FastQC/after_clipping", mode: 'copy',
         saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
 
-    when: !params.bam && !params.skip_adapterremoval
+    when: !params.bam && !params.skip_adapterremoval && !params.skip_fastqc
 
     input:
     set val(name), file(reads) from ch_clipped_reads_for_fastqc