Display sentieon dedup metrics in multiqc

assets/multiqc_config.yml

@@ -66,7 +66,38 @@ sample_names_replace:
   "\\.[0-9]{4}$": ".md" # should match ".0001" but only at the end of strings for module Markduplicates/EstimateLibraryComplexity
   module: picard
 
+custom_data:
+    dedup_metrics:
+        id: 'dedup_metrics'
+        section_name: 'Sentieon Dedup Metrics'
+        plot_type: 'table'
+        pconfig:
+            id: 'dedup_metrics'
+            namespace: 'Sentieon Dedup Metrics'
+        headers:
+            LIBRARY:
+                description: 'LIBRARY'
+            UNPAIRED_READS_EXAMINED:
+                description: 'UNPAIRED_READS_EXAMINE'
+            READ_PAIRS_EXAMINED:
+                description: 'READ_PAIRS_EXAMINED'
+            SECONDARY_OR_SUPPLEMENTARY_RDS:
+                description: 'SECONDARY_OR_SUPPLEMENTARY_RDS'
+            UNMAPPED_READS:
+                description: 'UNMAPPED_READS'
+            UNPAIRED_READ_DUPLICATES:
+                description: 'UNPAIRED_READ_DUPLICATES'
+            READ_PAIR_DUPLICATES:
+                description: 'READ_PAIR_DUPLICATES'
+            READ_PAIR_OPTICAL_DUPLICATES:
+                description: 'READ_PAIR_OPTICAL_DUPLICATES'
+            PERCENT_DUPLICATION:
+                description: 'PERCENT_DUPLICATION'
+            ESTIMATED_LIBRARY_SIZE:
+                description: 'ESTIMATED_LIBRARY_SIZE'
 sp:
   snpeff:
     contents: "SnpEff_version"
     max_filesize: 5000000
+  dedup_metrics:
+    fn: "*.metrics.multiqc.tsv"

conf/modules/sentieon_dedup.config

@@ -28,7 +28,7 @@ process {
             [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/reports/" },
-                pattern: "*metrics",
+                pattern: "*{metrics,metrics.multiqc.tsv}",
                 saveAs: { !(params.skip_tools && params.skip_tools.split(',').contains('sentieon_dedup_report')) ? "sentieon_dedup/${meta.id}/${it}" : null}
             ]
         ]

modules.json

@@ -384,7 +384,8 @@
                     "sentieon/dedup": {
                         "branch": "master",
                         "git_sha": "2cb2012b268b3502ac74463e510e76be99e2cdbf",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/sentieon/dedup/sentieon-dedup.diff"
                     },
                     "sentieon/gvcftyper": {
                         "branch": "master",

subworkflows/local/bam_sentieon_dedup/main.nf

@@ -34,6 +34,7 @@ workflow BAM_SENTIEON_DEDUP {
 
     // Gather all reports generated
     reports = reports.mix(SENTIEON_DEDUP.out.metrics)
+    reports = reports.mix(SENTIEON_DEDUP.out.metrics_multiqc_tsv)
     reports = reports.mix(SENTIEON_DEDUP.out.score)
     reports = reports.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.reports)
 

tests/test_sentieon_dedup_from_bam.yml

@@ -13,6 +13,8 @@
     - path: results/csv/recalibrated.csv
       md5sum: 1888a924bc70bd80165a96ad641e22d6
     - path: results/multiqc
+    - path: results/multiqc/multiqc_report.html
+      contains: ["Sentieon Dedup Metrics", "PERCENT_DUPLICATION", "ESTIMATED_LIBRARY_SIZE"]
     - path: results/preprocessing/sentieon_dedup/test/test.md.cram
     # binary changes md5sums on reruns
     - path: results/preprocessing/sentieon_dedup/test/test.md.cram.crai

tests/test_sentieon_dedup_from_cram.yml

@@ -13,6 +13,8 @@
     - path: results/csv/recalibrated.csv
       md5sum: 1888a924bc70bd80165a96ad641e22d6
     - path: results/multiqc
+    - path: results/multiqc/multiqc_report.html
+      contains: ["Sentieon Dedup Metrics", "PERCENT_DUPLICATION", "ESTIMATED_LIBRARY_SIZE"]
     - path: results/preprocessing/sentieon_dedup/test/test.md.cram
     # binary changes md5sums on reruns
     - path: results/preprocessing/sentieon_dedup/test/test.md.cram.crai