Add multiqc step

main.nf

 #!/usr/bin/env nextflow
 
 params.location = 's3://lj-nf-fastq-testdata/data/*.fastq.gz'
-Channel.fromPath(params.location).set{ch_fastqs}
+params.publish = 's3://lj-nf-fastq-testdata/results/'
+Channel.fromPath(params.location).into{ch_fastqs1}
+
+process run_fastqc {
+
+    publishDir params.publish
 
-process debug_print_file_name {
-    echo true
     input:
-    file f from ch_fastqs
+    file f from ch_fastqs1
+
+    output:
+    file "*.zip" into ch_qc_reports
+
+    script:
+    """
+    fastqc $f
+    """
+
+}
+
+process run_multiqc {
+    
+    publishDir params.publish
+
+    input:
+    file f from ch_qc_reports.collect()
+
+    output:
+    file "multiqc*" into ch_multiqc_result
 
     script:
     """
-    echo $f
+    multiqc $f
     """
 }