Modify MULTIQC: separate logo from config file (#2027)

* Separate MultiQC config from logo input channel

* Update meta.yml

* Update main.nf

* Add test for new check

* md5sum -> contains

modules/multiqc/main.nf

@@ -8,7 +8,8 @@ process MULTIQC {
 
     input:
     path  multiqc_files, stageAs: "?/*"
-    tuple path(multiqc_config), path(multiqc_logo)
+    path(multiqc_config)
+    path(multiqc_logo)
 
     output:
     path "*multiqc_report.html", emit: report

modules/multiqc/meta.yml

@@ -19,11 +19,11 @@ input:
         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
+      description: Optional config yml for MultiQC
       pattern: "*.{yml,yaml}"
   - multiqc_logo:
       type: file
-      description: Logo file for MultiQC
+      description: Optional logo file for MultiQC
       pattern: "*.{png}"
 output:
   - report:

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 {
@@ -29,5 +29,17 @@ 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 {
+    input = [
+        [ id: 'test', single_end: false ],
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+    mqc_config = file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)
+    mqc_input = Channel.empty()
+
+    FASTQC  ( input )
+    MULTIQC ( FASTQC.out.zip.collect { it[1] }, mqc_config,[] )
 }

tests/modules/multiqc/test.yml

@@ -3,11 +3,39 @@
   tags:
     - multiqc
   files:
+    - path: output/multiqc/multiqc_data/multiqc.log
+      contains: ["MultiQC complete"]
+    - path: output/multiqc/multiqc_data/multiqc_citations.txt
+      contains: ["10.1093/bioinformatics/btw354"]
+    - path: output/multiqc/multiqc_data/multiqc_data.json
+      contains: ["report_data_sources"]
     - path: output/multiqc/multiqc_report.html
+      contains: ["Abandon hope all ye who enter here.."]
 
 - name: multiqc test_multiqc_fn_collision
   command: nextflow run ./tests/modules/multiqc -entry test_multiqc_fn_collision -c ./tests/config/nextflow.config  -c ./tests/modules/multiqc/nextflow.config
   tags:
     - multiqc
   files:
+    - path: output/multiqc/multiqc_data/multiqc.log
+      contains: ["MultiQC complete"]
+    - path: output/multiqc/multiqc_data/multiqc_citations.txt
+      contains: ["10.1093/bioinformatics/btw354"]
+    - path: output/multiqc/multiqc_data/multiqc_data.json
+      contains: ["report_data_sources"]
     - path: output/multiqc/multiqc_report.html
+      contains: ["Abandon hope all ye who enter here.."]
+
+- name: multiqc test_multiqc_config
+  command: nextflow run ./tests/modules/multiqc -entry test_multiqc_config -c ./tests/config/nextflow.config  -c ./tests/modules/multiqc/nextflow.config
+  tags:
+    - multiqc
+  files:
+    - path: output/multiqc/multiqc_data/multiqc.log
+      contains: ["MultiQC complete"]
+    - path: output/multiqc/multiqc_data/multiqc_citations.txt
+      contains: ["10.1093/bioinformatics/btw354"]
+    - path: output/multiqc/multiqc_data/multiqc_data.json
+      contains: ["report_data_sources"]
+    - path: output/multiqc/multiqc_report.html
+      contains: ["Abandon hope all ye who enter here.."]