Add MultiQC index section to navigate between reports

.nf-core.yml

@@ -1,5 +1,6 @@
 lint:
   actions_ci: false
+  multiqc_config: false
   files_unchanged:
     - .github/CONTRIBUTING.md
   files_exist:

CHANGELOG.md

@@ -23,6 +23,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
+- [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125)
 
 ### `Fixed`
 

assets/multiqc_config.yml

@@ -3,9 +3,11 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
+  "nf-core-seqinspector-index":
+    order: -999
   "nf-core-seqinspector-methods-description":
     order: -1000
-  software_versions:
+  multiqc_software_versions:
     order: -1001
   "nf-core-seqinspector-summary":
     order: -1002

subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf

@@ -275,3 +275,34 @@ def methodsDescriptionText(mqc_methods_yaml) {
     return description_html.toString()
 }
 
+//
+// Generate report index for MultiQC
+//
+def reportIndexMultiqc(tags, global=true) {
+    def relative_path = global ? ".." : "../.."
+
+    def a_attrs = "target=\"_blank\" class=\"list-group-item list-group-item-action\""
+
+    // Global report path
+    def index_section = "    <a href=\"${relative_path}/global_report/multiqc_report.html\" ${a_attrs}>Global report</a>\n"
+
+    // Group report paths
+    tags
+        .each { tag ->
+            index_section += "    <a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\" ${a_attrs}>Group report: ${tag}</a>\n"
+        }
+
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-index'\n" as String
+    yaml_file_text     += "description: 'MultiQC reports collected from running the pipeline.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} MultiQC Reports Index'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "  <h4>Reports</h4>\n"
+    yaml_file_text     += "  <p>Select a report to view (open in a new tab):</p>\n"
+    yaml_file_text     += "  <div class=\"list-group\">\n"
+    yaml_file_text     += "${index_section}"
+    yaml_file_text     += "  </div>\n"
+
+    return yaml_file_text
+}

workflows/seqinspector.nf

@@ -20,6 +20,7 @@ include { paramsSummaryMap              } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { reportIndexMultiqc            } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -148,6 +149,11 @@ workflow SEQINSPECTOR {
     //
     // MODULE: MultiQC
     //
+    ch_tags = ch_multiqc_files
+        .map { meta, _sample -> meta.tags }
+        .flatten()
+        .unique()
+
     ch_multiqc_config = params.multiqc_config ?
         Channel.fromPath(params.multiqc_config, checkIfExists: true) :
         Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
@@ -174,11 +180,22 @@ workflow SEQINSPECTOR {
             sort: true
         )
     )
+    // Add index to other MultiQC reports
+    //ch_multiqc_extra_files_global = Channel.empty()
+    ch_multiqc_extra_files_global = ch_multiqc_extra_files.mix(
+        ch_tags.toList()
+            .map { tag_list ->
+                reportIndexMultiqc(tag_list)
+            }
+            .collectFile(
+                name: 'multiqc_index_mqc.yaml',
+            )
+    )
 
     MULTIQC_GLOBAL (
         ch_multiqc_files
             .map { meta, file -> file }
-            .mix(ch_multiqc_extra_files)
+            .mix(ch_multiqc_extra_files_global)
             .collect(),
         ch_multiqc_config.toList(),
         [],
@@ -187,13 +204,18 @@ workflow SEQINSPECTOR {
         []
     )
 
-    ch_tags = ch_multiqc_files
-        .map { meta, _sample -> meta.tags }
-        .flatten()
-        .unique()
+    ch_multiqc_extra_files_tag = ch_multiqc_extra_files.mix(
+        ch_tags.toList()
+            .map { tag_list ->
+                reportIndexMultiqc(tag_list, false)
+            }
+            .collectFile(
+                name: 'multiqc_index_mqc.yaml',
+            )
+    )
 
     multiqc_extra_files_per_tag = ch_tags
-        .combine(ch_multiqc_extra_files)
+        .combine(ch_multiqc_extra_files_tag)
 
     // Group samples by tag
     tagged_mqc_files = ch_tags
@@ -222,6 +244,7 @@ workflow SEQINSPECTOR {
             config: config
         }
 
+
     MULTIQC_PER_TAG(
         tagged_mqc_files.samples_per_tag,
         ch_multiqc_config.toList(),