Add new custom tables to multiqc #72

CHANGELOG.md

-# v0.0.2 (in development)
+# v0.0.3 (in development)
+**User Facing**
+* TPM table:
+  * Add Ensembl Gene ID
+  * Rename columns: *GENCODE_Gene_Symbol*, *Ensembl_GeneID*, *NCBI_GeneID*
+* MultiQC output custom talbes (html+JSON):
+  * Run table: *Session ID* and *Pipeline Version*
+  * Reference Table: *Species*, *Genome Reference Consortium Build*, *Genome Reference Consortium Patch*, *GENCODE Annotation Release* (ouputs both human and mouse versions)
+
+**Background**
+* Add GeneSymbol/EnsemblID/EntrezID translation files to references
+
+*Known Bugs*
+* outputBag does not contain fetch for processed data
+* Does not include automatic data upload
+
+<hr>
+
+# v0.0.2
 **User Facing**
 * Output:
   * inputBag

workflow/conf/multiqc_config.yaml

@@ -48,14 +48,28 @@ top_modules:
         - '*infer_experiment*'
 
 report_section_order:
+    run:
+      order: 4000
     rid:
-      order: 2000
+      order: 3000
     meta:
+      order: 2000
+    ref:
       order: 1000
 
 skip_generalstats: true
 
 custom_data:
+    run:
+        file_format: 'tsv'
+        section_name: 'Run'
+        description: 'This is the run information'
+        plot_type: 'table'
+        pconfig:
+            id: 'run'
+            format: '{:,.0f}'
+        headers:
+            Session ID
     rid:
         file_format: 'tsv'
         section_name: 'RID'
@@ -74,6 +88,7 @@ custom_data:
         plot_type: 'table'
         pconfig:
             id: 'meta'
+            scale: false
             format: '{:,.0f}'
         headers:
             Source
@@ -85,6 +100,21 @@ custom_data:
             Assigned Reads
             Median Read Length
             Median TIN
+            Pipeline Version
+    ref:
+        file_format: 'tsv'
+        section_name: 'Reference'
+        description: 'This is the referenec version information'
+        plot_type: 'table'
+        pconfig:
+            id: 'ref'
+            scale: false
+            format: '{}'
+        headers:
+            Species
+            Genome Reference Consortium Build
+            Genome Reference Consortium Patch
+            GENCODE Annotation Release"
     tin:
         file_format: 'tsv'
         section_name: 'TIN'
@@ -106,9 +136,13 @@ custom_data:
             90 - 99
 
 sp:
+    run:
+        fn: "run.tsv"
     rid:
         fn: 'rid.tsv'
     meta:
         fn: 'metadata.tsv'
+    ref:
+        fn: 'reference.tsv'
     tin:
-        fn: '*.tin.hist.tsv'
+        fn: '*.tin.hist.tsv'
\ No newline at end of file

workflow/nextflow.config

@@ -97,6 +97,6 @@ manifest {
   homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
   description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
   mainScript = 'rna-seq.nf'
-  version = 'v0.0.2_indev'
+  version = 'v0.0.3_indev'
   nextflowVersion = '>=19.09.0'
 }

workflow/rna-seq.nf

@@ -1034,6 +1034,11 @@ process aggrQC {
     hostname > ${repRID}.aggrQC.log
     ulimit -a >> ${repRID}.aggrQC.log
 
+    # make run table
+    echo -e "LOG: creating run table" >> ${repRID}.aggrQC.log
+    echo -e "Session ID\tPipeline Version" > run.tsv
+    echo -e "${workflow.sessionId}\t${workflow.manifest.version}" >> run.tsv
+    
     # make RID table
     echo -e "LOG: creating RID table" >> ${repRID}.aggrQC.log
     echo -e "Replicate RID\tExperiment RID\tStudy RID" > rid.tsv
@@ -1046,6 +1051,12 @@ process aggrQC {
     echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
     echo -e "Measured\t-\t${endsManual}\t-\t-\t'${rawReadsI}'\t'${assignedReadsI}'\t'${readLengthI}'\t'${tinMedI}'" >> metadata.tsv
 
+    # make reference table
+    echo -e "LOG: creating referencerun table" >> ${repRID}.aggrQC.log
+    echo -e "Species\tGenome Reference Consortium Build\tGenome Reference Consortium Patch\tGENCODE Annotation Release" > reference.tsv
+    echo -e "Human\tGRCh\$(echo `echo ${params.refHuVersion} | cut -d "." -f 1`)\t\$(echo `echo ${params.refHuVersion} | cut -d "." -f 2`)\t'\$(echo `echo ${params.refHuVersion} | cut -d "." -f 3 | sed "s/^v//"`)'" >> reference.tsv
+    echo -e "Mouse\tGRCm\$(echo `echo ${params.refMoVersion} | cut -d "." -f 1`)\t\$(echo `echo ${params.refMoVersion} | cut -d "." -f 2`)\t'\$(echo `echo ${params.refMoVersion} | cut -d "." -f 3 | sed "s/^v//"`)'" >> reference.tsv
+
     # remove inner distance report if it is empty (SE repRID)
     echo -e "LOG: removing dummy inner distance file" >> ${repRID}.aggrQC.log
     if [ "${endsM}" == "se" ]
@@ -1081,5 +1092,4 @@ process outputBag {
   cp ${multiqcJSON} Replicate_${repRID}.outputBag
   bdbag Replicate_${repRID}.outputBag --archiver zip
   """
-}
-
+}
\ No newline at end of file