diff --git a/README.md b/README.md
index 88d6664..cde7886 100644
--- a/README.md
+++ b/README.md
@@ -17,3 +17,13 @@ fastq-screen containers, so this is a temporary workaround for that. Here's how
  - Download fastqc-screen from  [here](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.13.0.tar.gz).
  - Uncompress it
  - Run `fastq_screen --get_genomes`
+
+
+# How to run the nextflow pipeline
+Awesome, you're all set! Let's try generating reports for your favourite runfolder:
+```
+cd nextflow
+nextflow -c config/nextflow.config run run_multiqc_nextflow.nf \
+          --runfolder ~/large_disk/180126_HSX122_0568_BHLFWLBBXX_small/ \
+          --fastq_screen_db ~/large_disk/FastQ_Screen_Genomes/
+```
diff --git a/nextflow/config/multiqc_flowcell_config.yaml b/nextflow/config/multiqc_flowcell_config.yaml
new file mode 100644
index 0000000..3a2c794
--- /dev/null
+++ b/nextflow/config/multiqc_flowcell_config.yaml
@@ -0,0 +1,24 @@
+# Config for flowcell Reports
+
+subtitle: "SNP&SEQ Technology Platform"
+intro_text: |
+  This is a report containing quality control information about your project run at the SNP&SEQ Technology
+  Platform. If you have any questions, please do not hesitate to contact us at
+  <a href="mailto:seq@medsci.uu.se">seq@medsci.uu.se</a>
+
+custom_logo: 'assets/UU_logo_tranp4f125px.png'
+custom_logo_url: 'http://sequencing.se'
+custom_logo_title: 'SNP&SEQ Technology Platform'
+
+table_columns_visible:
+    FastQC:
+        percent_duplicates: False
+        percent_gc: False
+        total_sequences: False
+
+top_modules:
+    - 'bcl2fastq'
+    - 'interop'
+
+remove_sections:
+    - 'fastqc_sequence_counts'
diff --git a/nextflow/config/multiqc_config.yaml b/nextflow/config/multiqc_project_config.yaml
similarity index 55%
rename from nextflow/config/multiqc_config.yaml
rename to nextflow/config/multiqc_project_config.yaml
index 82431b9..0ae96d8 100644
--- a/nextflow/config/multiqc_config.yaml
+++ b/nextflow/config/multiqc_project_config.yaml
@@ -1,5 +1,4 @@
-# QC criteria for NGI Uppsala, based on values in INS-00123
-# Compatible with MultiQC v1.6
+# Config for project reports
 
 subtitle: "SNP&SEQ Technology Platform"
 intro_text: |
@@ -11,7 +10,6 @@ custom_logo: 'assets/UU_logo_tranp4f125px.png'
 custom_logo_url: 'http://sequencing.se'
 custom_logo_title: 'SNP&SEQ Technology Platform'
 
-
 clarity:
     name_edit_regex: '^.*.\/(.*)_L00\d_[R|I]\d_001\.fastq\.gz$'
 
@@ -43,57 +41,9 @@ clarity:
 #            'Insert size (bp)':
 #                description: 'Target insert size'
 
+table_columns_visible:
+    FastQC:
+        percent_duplicates: False
 
-
-max_table_rows: 1000
-
-table_cond_formatting_rules:
-    mqc-generalstats-qualimap-percentage_aligned:
-        pass:
-            - gt: 97.1
-        fail:
-            - lt: 97.1
-
-    mqc-generalstats-qualimap-avg_gc:
-        pass:
-            - gt: 40.5
-            - lt: 42.1
-        fail:
-            - lt: 40.5
-            - gt: 42.1
-
-    mqc-generalstats-qualimap-median_insert_size: 
-        pass:
-            - gt: 317
-            - lt: 428 
-        fail:
-            - lt: 317
-            - gt: 428
-
-    mqc-generalstats-qualimap-10_x_pc: 
-        pass:
-            - gt: 91
-        fail:
-            - lt: 91
-    
-    mqc-generalstats-qualimap-30_x_pc: 
-        pass:
-            - gt: 58
-        fail:
-            - lt: 58
-
-    mqc-generalstats-snpeff-Number_of_variants_before_filter: 
-        pass:
-            - gt: 4.8
-            - lt: 5.3
-        fail:
-            - lt: 4.8
-            - gt: 5.3
-
-    mqc-generalstats-snpeff-Ts_Tv_ratio: 
-        pass:
-            - gt: 1.98
-            - lt: 2.01
-        fail:
-            - lt: 1.98
-            - gt: 2.01
+remove_sections:
+    - 'fastqc_sequence_counts'
diff --git a/nextflow/run_multiqc_nextflow.nf b/nextflow/run_multiqc_nextflow.nf
index d937f6e..af8e1bf 100644
--- a/nextflow/run_multiqc_nextflow.nf
+++ b/nextflow/run_multiqc_nextflow.nf
@@ -36,8 +36,11 @@ Channel
 params.fastq_screen_config = "config/fastq_screen.conf"
 fastq_screen_config = file(params.fastq_screen_config)
 
-params.multiqc_config = "config/multiqc_config.yaml"
-multiqc_config = file(params.multiqc_config)
+params.multiqc_flowcell_config = "config/multiqc_flowcell_config.yaml"
+multiqc_flowcell_config = file(params.multiqc_flowcell_config)
+
+params.multiqc_project_config = "config/multiqc_project_config.yaml"
+multiqc_project_config = file(params.multiqc_project_config)
 
 fastq_screen_db = file(params.fastq_screen_db)
 
@@ -107,7 +110,7 @@ process MultiQCPerFlowcell {
     file (fastqscreen:'FastQScreen/*') from fastq_screen_results_for_flowcell.map{ it.get(1) }.collect().ifEmpty([])
     file (interop_summary:'Interop_summary/*') from interop_summary_results.collect().ifEmpty([])
     file runfolder
-    file config from multiqc_config
+    file config from multiqc_flowcell_config
     file assets from assets
 
     output:
@@ -141,7 +144,7 @@ process MultiQCPerProject {
     input:
     set project, file(fastqc: "*") from fastqc_results_for_project_grouped_by_project
     set project_fastq_screen, file(fastqc_screen: "*") from fastq_screen_results_for_project_grouped_by_project
-    file config from multiqc_config
+    file config from multiqc_project_config
     file runfolder
     file assets from assets