Fix MultiQC

conf/test_nothing.config

@@ -12,7 +12,7 @@
 
 params {
     config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others'
+    config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others"
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2

modules.json

@@ -115,7 +115,7 @@
                 },
                 "multiqc": {
                     "branch": "master",
-                    "git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106"
+                    "git_sha": "16eee433b87b303bda650131ac5a0b1ad725e166"
                 },
                 "porechop": {
                     "branch": "master",

modules/nf-core/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/nf-core/modules/multiqc/meta.yml

@@ -12,6 +12,7 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+
 input:
   - multiqc_files:
       type: file
@@ -19,12 +20,13 @@ 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:
       type: file
@@ -46,3 +48,4 @@ authors:
   - "@abhi18av"
   - "@bunop"
   - "@drpatelh"
+  - "@jfy133"

workflows/taxprofiler.nf

@@ -42,8 +42,7 @@ if (params.run_malt && params.run_krona && !params.krona_taxonomy_directory) log
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ch_multiqc_config   = params.multiqc_config ? file( params.multiqc_config, checkIfExists: true ) : file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -93,7 +92,7 @@ def multiqc_report = []
 workflow TAXPROFILER {
 
     ch_versions = Channel.empty()
-    ch_taxprofiler_logo = Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
+    ch_multiqc_logo= Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
 
     /*
         SUBWORKFLOW: Read in samplesheet, validate and stage input files
@@ -241,14 +240,11 @@ workflow TAXPROFILER {
     ch_workflow_summary = Channel.value(workflow_summary)
 
     ch_multiqc_files = Channel.empty()
-    ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
+
-    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
 
-    ch_multiqc_files = ch_multiqc_files.mix(ch_taxprofiler_logo.ifEmpty([]))
-
     if (params.perform_shortread_qc) {
         ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
     }
@@ -269,7 +265,9 @@ workflow TAXPROFILER {
 
     // TODO create multiQC module for metaphlan
     MULTIQC (
-        ch_multiqc_files.collect(), [[], []]
+        ch_multiqc_files.collect(),
+        ch_multiqc_config,
+        ch_multiqc_logo
     )
     multiqc_report = MULTIQC.out.report.toList()
     ch_versions    = ch_versions.mix(MULTIQC.out.versions)