Add metadata and repRID to multiqc report

workflow/conf/multiqc_config.yaml

@@ -13,6 +13,7 @@ report_comment: >
   This report has been generated by the <a href="https://doi.org/10.5281/zenodo.3625056">GUDMAP/RBK RNA-Seq Pipeline</a>
 
 top_modules:
+  - custom_content
   - fastqc:
       name: 'Raw'
       info: 'Replicate Raw fastq QC Results'
@@ -35,9 +36,6 @@ top_modules:
       info: 'Replicate Paired End Inner Distance Distribution Results'
       path_filters:
         - '*insertSize*'
-  - custom_content:
-      name: 'TIN'
-      info: 'Transcript Integrety Score Distribution Results'
   - hisat2:
       name: 'Inference: Align'
       info: 'Inference Alignment (1M downsampled reads) QC Results'
@@ -49,9 +47,41 @@ top_modules:
       path_filters:
         - '*infer_experiment*'
 
+report_section_order:
+    rid:
+      order: 200
+    meta:
+      order: 100
+    tin:
+      order: -100
+
 skip_generalstats: true
 
 custom_data:
+    rid:
+        file_format: 'tsv'
+        section_name: 'RID'
+        description: 'This is the identifying RIDs'
+        plot_type: 'table'
+        pconfig:
+            id: 'rid'
+        headers:
+            Replicate RID
+            Experiment RID
+            Study RID
+    meta:
+        file_format: 'tsv'
+        section_name: 'Metadata'
+        description: 'This is the comparison of infered metadata and submitter provided'
+        plot_type: 'table'
+        pconfig:
+            id: 'meta'
+        headers:
+            Source
+            Species
+            Ends
+            Stranded
+            Spike-in
     tin:
         file_format: 'tsv'
         section_name: 'TIN'
@@ -71,6 +101,11 @@ custom_data:
             70 - 79
             80 - 89
             90 - 99
+
 sp:
+    rid:
+        fn: 'rid.tsv'
+    meta:
+        fn: 'metadata.tsv'
     tin:
         fn: '*.tin.hist.tsv'

workflow/rna-seq.nf

@@ -223,6 +223,7 @@ endsManual.into {
   endsManual_trimData
   endsManual_downsampleData
   endsManual_alignSampleData
+  endsManual_aggrQC
 }
 
 
@@ -533,16 +534,20 @@ endsInfer.into {
   endsInfer_alignData
   endsInfer_countData
   endsInfer_dataQC
+  endsInfer_aggrQC
 }
 strandedInfer.into {
   strandedInfer_alignData
   strandedInfer_countData
+  strandedInfer_aggrQC
 }
 spikeInfer.into{
   spikeInfer_getRef
+  spikeInfer_aggrQC
 }
 speciesInfer.into {
   speciesInfer_getRef
+  speciesInfer_aggrQC
 }
 
 
@@ -872,7 +877,7 @@ process dataQC {
     # bin TIN values
     python3 ${script_tinHist} -r ${repRID}
 
-    # calculate inner-distances for PE dat
+    # calculate inner-distances for PE data
     if [ "${ends}" == "pe" ]
     then
       inner_distance.py -i "${bam}" -o ${repRID}.insertSize -r ./bed/genome.bed 1>>${repRID}.dataQC.out 2>>${repRID}.dataQC.err
@@ -896,10 +901,19 @@ process aggrQC {
     path alignQC
     path dedupQC
     path countsQC
-    path tin
     path innerDistance
+    path tin
     path alignSampleQCs from alignSampleQC_aggrQC.collect()
     path inferExperiment
+    val endsManual from endsManual_aggrQC
+    val endsM from endsMeta
+    val strandedM from strandedMeta
+    val spikeM from spikeMeta
+    val speciesM from speciesMeta
+    val endsI from endsInfer_aggrQC
+    val strandedI from strandedInfer_aggrQC
+    val spikeI from spikeInfer_aggrQC
+    val speciesI from speciesInfer_aggrQC
 
   output:
     path "${repRID}.aggrQC.{out,err}" optional true
@@ -909,10 +923,21 @@ process aggrQC {
     hostname > ${repRID}.aggrQC.err
     ulimit -a >> ${repRID}.aggrQC.err
 
+    echo -e "Replicate RID\tExperiment RID\tStudy RID" > rid.tsv
+    echo -e "${repRID}\t-\t-" >> rid.tsv
+
+    echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in" > metadata.tsv
+    echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}" >> metadata.tsv
+    echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}" >> metadata.tsv
+    echo -e "Manual\t-\t${endsManual}\t-\t-" >> metadata.tsv
+
+    # remove inner distance report if it is empty (SE repRID)
     if [ wc -l ${innerDistance} | awk '{print\${1}}' -eq 0 ]
     then
       rm -f ${innerDistance}
     fi
+
+    #run MultiQC
     multiqc -c ${multiqcConfig} .
     """
 }