Merge pull request #57 from grst/multiqc

Add MultiQC report

conf/modules.config

@@ -30,6 +30,15 @@ process {
         ]
     }
 
+    // store sample-specifc results in the per-sample subfolder
+    withName: FASTQC {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: SPACERANGER_COUNT {
         publishDir = [
             // NOTE: the sample name is already excluded in the path that's getting published.

lib/WorkflowSpatialtranscriptomics.groovy

@@ -2,6 +2,9 @@
 // This file holds several functions specific to the workflow/spatialtranscriptomics.nf in the nf-core/spatialtranscriptomics pipeline
 //
 
+import nextflow.Nextflow
+import groovy.text.SimpleTemplateEngine
+
 class WorkflowSpatialtranscriptomics {
 
     //
@@ -14,4 +17,48 @@ class WorkflowSpatialtranscriptomics {
         // }
     }
 
+    //
+    // Get workflow summary for MultiQC
+    //
+    public static String paramsSummaryMultiqc(workflow, summary) {
+        String summary_section = ''
+        for (group in summary.keySet()) {
+            def group_params = summary.get(group)  // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                for (param in group_params.keySet()) {
+                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                }
+                summary_section += "    </dl>\n"
+            }
+        }
+
+        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+        yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
+        yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+        yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+        yaml_file_text        += "plot_type: 'html'\n"
+        yaml_file_text        += "data: |\n"
+        yaml_file_text        += "${summary_section}"
+        return yaml_file_text
+    }
+
+    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
+        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+        def meta = [:]
+        meta.workflow = run_workflow.toMap()
+        meta["manifest_map"] = run_workflow.manifest.toMap()
+
+        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
+        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+        def methods_text = mqc_methods_yaml.text
+
+        def engine =  new SimpleTemplateEngine()
+        def description_html = engine.createTemplate(methods_text).make(meta)
+
+        return description_html
+    }
+
 }

modules.json

@@ -8,8 +8,17 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
+                        "installed_by": ["modules"]
+                    },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
                     },
                     "spaceranger/count": {
                         "branch": "master",