update mqc inputs

modules/multiqc/main.nf

@@ -7,7 +7,8 @@ process MULTIQC {
         'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
 
     input:
-    path "*/*"
+    path  multiqc_files, stageAs: "?/*"
+    tuple path(mqc_config), path(mqc_logo)
 
     output:
     path "*multiqc_report.html", emit: report

modules/multiqc/meta.yml

@@ -17,6 +17,14 @@ input:
       type: file
       description: |
         List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Logo file for MultiQC
+      pattern: "*.{png}"
 output:
   - report:
       type: file

tests/modules/multiqc/main.nf

@@ -12,7 +12,7 @@ workflow test_multiqc {
             ]
 
     FASTQC  ( input )
-    MULTIQC ( FASTQC.out.zip.collect { it[1] } )
+    MULTIQC ( FASTQC.out.zip.collect { it[1] }, [[],[]] )
 }
 
 workflow test_multiqc_fn_collision {
@@ -27,5 +27,5 @@ workflow test_multiqc_fn_collision {
     FASTQC2  ( fqc_input )
     mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
 
-    MULTIQC ( mqc_input )
+    MULTIQC ( mqc_input, [[],[]] )
 }