Include DRAGEN metrics in MULTIQC report

.nf-core.yml

@@ -0,0 +1 @@
+repository_type: pipeline

CHANGELOG.md

@@ -9,9 +9,13 @@ Initial release of nf-core/dragen, created with the [nf-core](https://nf-co.re/)
 
 ### `Added`
 
+- Publish csv outputs from `DRAGEN` for `multiQC` module
+- Stub runs for `DRAGEN`, including creation of a file recognised by the `multiQC` module
+
 ### `Fixed`
 
 - Fixed error `Access to 'FASTQC.out' is undefined since the workflow 'FASTQC' has not been invoked before accessing the output attribute` when `-skip_fastqc` enabled by adjusting channel generation
+- Added `arm` profile for docker runs on Mac OS
 
 ### `Dependencies`
 

assets/methods_description_template.yml

@@ -0,0 +1,25 @@
+id: "seqeralabs-dragen-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "seqeralabs/nf-dragen Methods Description"
+section_href: "https://github.com/seqeralabs/nf-dragen"
+plot_type: "html"
+## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## You inject any metadata in the Nextflow '${workflow}' object
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using seqeralabs/nf-dragen v${workflow.manifest.version}.</p>
+  <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
+  <pre><code>${workflow.commandLine}</code></pre>
+  <h4>References</h4>
+  <ul>
+    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
+    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+  </ul>
+  <div class="alert alert-info">
+    <h5>Notes:</h5>
+    <ul>
+      ${nodoi_text}
+      <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+    </ul>
+  </div>

conf/modules.config

@@ -65,7 +65,7 @@ if (!params.skip_dragen) {
 
         withName: 'DRAGEN_FASTQ_TO_BAM_DNA' {
             publishDir = [
-                path: { "${params.outdir}/dragen/dna_fastq_to_bam" },
+                path: { "${params.outdir}/dragen/dna_fastq_to_bam/${meta.id}/" },
                 mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -74,7 +74,7 @@ if (!params.skip_dragen) {
         withName: 'DRAGEN_FASTQ_TO_VCF_DNA' {
             ext.args = '--enable-variant-caller true'
             publishDir = [
-                path: { "${params.outdir}/dragen/dna_fastq_to_vcf" },
+                path: { "${params.outdir}/dragen/dna_fastq_to_vcf/${meta.id}/" },
                 mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -83,7 +83,7 @@ if (!params.skip_dragen) {
         withName: 'DRAGEN_FASTQ_TO_BAM_RNA' {
             ext.args = '--enable-rna true'
             publishDir = [
-                path: { "${params.outdir}/dragen/rna_fastq_to_bam" },
+                path: { "${params.outdir}/dragen/rna_fastq_to_bam/${meta.id}/" },
                 mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]

lib/WorkflowDragen.groovy

@@ -2,6 +2,8 @@
 // This file holds several functions specific to the workflow/dragen.nf in the nf-core/dragen pipeline
 //
 
+import groovy.text.SimpleTemplateEngine
+
 class WorkflowDragen {
 
     //
@@ -43,6 +45,23 @@ class WorkflowDragen {
         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
+    }
+
     //
     // Exit pipeline if incorrect --genome key provided
     //

modules.json

@@ -1,17 +1,31 @@
 {
-    "name": "nf-core/dragen",
-    "homePage": "https://github.com/nf-core/dragen",
+    "name": "nf-dragen",
+    "homePage": "https://github.com/drpatelh/nf-dragen",
     "repos": {
-        "nf-core/modules": {
-            "custom/dumpsoftwareversions": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+        "https://github.com/nf-core/modules.git": {
+            "modules": {
+                "nf-core": {
+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b",
+                        "installed_by": ["modules"]
+                    },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["modules"]
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/multiqc/multiqc.diff"
+                    }
+                }
             },
-            "fastqc": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-            },
-            "multiqc": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+            "subworkflows": {
+                "nf-core": {}
             }
         }
     }
-}
+}

modules/local/dragen.nf

@@ -16,6 +16,7 @@ process DRAGEN {
     tuple val(meta), path("${prefix}.vcf.gz.tbi")              , emit: tbi         , optional:true
     tuple val(meta), path("${prefix}.hard-filtered.vcf.gz")    , emit: vcf_filtered, optional:true
     tuple val(meta), path("${prefix}.hard-filtered.vcf.gz.tbi"), emit: tbi_filtered, optional:true
+    tuple val(meta), path("${prefix}.*.csv")                   , emit: csv , optional:true
     path  "versions.yml"                                       , emit: versions
 
     script:
@@ -52,4 +53,33 @@ process DRAGEN {
         dragen: \$(echo \$(/opt/edico/bin/dragen --version 2>&1) | sed -e "s/dragen Version //g")
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    // Generate stub files
+    // Include one possible csv file, and faked data to prompt multiqc
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+    touch ${prefix}.hard-filtered.vcf.gz
+    touch ${prefix}.hard-filtered.vcf.gz.tbi
+
+    # Define the header row of the CSV file
+    echo "RUN TIME,,Time loading reference,00:00.1,0.09" > ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Time aligning reads,00:00.5,0.53" >> ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Time sorting,00:00.4,0.38" >> ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Time DRAGStr calibration,00:00.0,0" >> ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Time saving map/align output,00:05.6,5.57" >> ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Time variant calling,00:05.5,5.45" >> ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Time partitioning,00:00.1,0.12" >> ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Time structural variant calling,00:02.8,2.83" >> ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Time accessing license server,00:13.2,13.21" >> ${prefix}.time_metrics.csv
+    echo "RUN TIME,,Total runtime,00:27.2,27.17" >> ${prefix}.time_metrics.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dragen: \$(echo "vSTUB")
+    END_VERSIONS
+    """
 }

modules/local/dragen_buildhashtable.nf

@@ -30,4 +30,15 @@ process DRAGEN_BUILDHASHTABLE {
         dragen: \$(echo \$(/opt/edico/bin/dragen --version 2>&1) | sed -e "s/dragen Version //g")
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: 'dragen'
+    """
+    mkdir -p $prefix
+    touch $prefix/dragen.ht
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dragen: \$(echo "v3.4.12")
+    END_VERSIONS
+    """
 }