Rename input and output parameter. Fix published data to only include html files

main.nf

 #!/usr/bin/env nextflow
 
-params.location = 's3://lj-nf-fastq-testdata/data/*.fastq.gz'
-params.publish = 's3://lj-nf-fastq-testdata/results/'
-Channel.fromPath(params.location).set{ch_fastqs1}
+params.input = "${baseDir}/example_data/*.fastq.gz"
+params.output = 'results'
+
+Channel.fromPath(params.input).set{ch_fastqs1}
 
 process run_fastqc {
-    publishDir params.publish
+    publishDir params.output + '/fastqc-reports', pattern: '*.html', mode: 'copy'
 
     input:
     file f from ch_fastqs1
 
     output:
-    file "*.zip" into ch_qc_reports
+    file "*.zip" into ch_qc_report_data
+    file "*.html" into ch_qc_reports
 
     script:
     """
@@ -21,13 +23,13 @@ process run_fastqc {
 }
 
 process run_multiqc {
-    publishDir params.publish
+    publishDir params.output + '/multiqc-report', mode: 'copy'
 
     input:
-    file f from ch_qc_reports.collect()
+    file f from ch_qc_report_data.collect()
 
     output:
-    file "multiqc*" into ch_multiqc_result
+    file "*.html" into ch_multiqc_report
 
     script:
     """