From 439d2a9e679977add51da377f3dbfdf68ab5c6a9 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 8 Jun 2022 13:48:27 +0200
Subject: [PATCH] update mqc inputs

---
 modules/multiqc/main.nf       | 3 ++-
 modules/multiqc/meta.yml      | 8 ++++++++
 tests/modules/multiqc/main.nf | 4 ++--
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
index d376db60..df68d853 100644
--- a/modules/multiqc/main.nf
+++ b/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
diff --git a/modules/multiqc/meta.yml b/modules/multiqc/meta.yml
index 6fa891ef..bf3a27fe 100644
--- a/modules/multiqc/meta.yml
+++ b/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
diff --git a/tests/modules/multiqc/main.nf b/tests/modules/multiqc/main.nf
index 3719d423..e015cbc3 100644
--- a/tests/modules/multiqc/main.nf
+++ b/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, [[],[]] )
 }