Update MULTIQC for an additional custom config (#2063)

* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Add support for secondary custom configs

modules/multiqc/main.nf

@@ -9,6 +9,7 @@ process MULTIQC {
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
+    path(extra_multiqc_config)
     path(multiqc_logo)
 
     output:
@@ -23,11 +24,13 @@ process MULTIQC {
     script:
     def args = task.ext.args ?: ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
+    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
     """
     multiqc \\
         --force \\
-        $config \\
         $args \\
+        $config \\
+        $extra_config \\
         .
 
     cat <<-END_VERSIONS > versions.yml

modules/multiqc/meta.yml

@@ -22,6 +22,10 @@ input:
       type: file
       description: Optional config yml for MultiQC
       pattern: "*.{yml,yaml}"
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
+      pattern: "*.{yml,yaml}"
   - multiqc_logo:
       type: file
       description: Optional logo file for MultiQC

tests/modules/multiqc/main.nf

@@ -13,7 +13,7 @@ workflow test_multiqc {
     ]
 
     FASTQC  ( input )
-    MULTIQC ( FASTQC.out.zip.collect { it[1] }, [], [] )
+    MULTIQC ( FASTQC.out.zip.collect { it[1] }, [], [], [] )
 }
 
 workflow test_multiqc_fn_collision {
@@ -29,7 +29,7 @@ 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, [], [], [] )
 }
 
 workflow test_multiqc_config {
@@ -41,5 +41,5 @@ workflow test_multiqc_config {
     mqc_input = Channel.empty()
 
     FASTQC  ( input )
-    MULTIQC ( FASTQC.out.zip.collect { it[1] }, mqc_config, [] )
+    MULTIQC ( FASTQC.out.zip.collect { it[1] }, mqc_config, [], [] )
 }