From d1271604f9c56261d3cb73a038fad5ed5063912a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 10:20:47 -0600
Subject: [PATCH] Add seqwho infer QC table to multiqc

---
 rna-seq.nf                        | 22 +++++++++++++++++-----
 workflow/conf/multiqc_config.yaml | 30 ++++++++++++++++++++++++++++--
 2 files changed, 45 insertions(+), 7 deletions(-)

diff --git a/rna-seq.nf b/rna-seq.nf
index 52c2a3f..35ecf9a 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -683,6 +683,7 @@ process seqwho {
     val fastqReadError from fastqReadError_seqwho
 
   output:
+    path "seqwhoInfer.tsv" into seqwhoInfer
     path "inferSpecies.csv" into inferSpecies_fl
     path "inferError.csv" into inferError_fl
 
@@ -828,6 +829,7 @@ process seqwho {
         seqtypeError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
         echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
       fi
+      consensus="-"
     else
       echo -e "LOG: low confidence seq type inference detected" >> ${repRID}.seqwho.log
       seqtk sample -s100 ${fastq[0]} 1000000 1> sampled.1.seed100.fastq &
@@ -845,9 +847,9 @@ process seqwho {
       cp SeqWho_call.tsv SeqWho_call_sampledR1.tsv
       if [ "\${seqtypeR1_1}" == "\${seqtypeR1}" ] && [ "\${seqtypeR1_2}" == "\${seqtypeR1}" ] && [ "\${seqtypeR1_3}" == "\${seqtypeR1}" ]
       then
-        concensus=true
+        consensus=true
       else
-        concensus=false
+        consensus=false
       fi
       if [ "${ends}" == "pe" ]
       then
@@ -866,12 +868,12 @@ process seqwho {
         cp SeqWho_call.tsv SeqWho_call_sampledR2.tsv
         if [ "\${seqtypeR2_1}" == "\${seqtypeR1}" ] && [ "\${seqtypeR2_2}" == "\${seqtypeR1}" ] && [ "\${seqtypeR2_3}" == "\${seqtypeR1}" ]
         then
-          concensus=\${concensus}
+          consensus=\${consensus}
         else
-          concensus=false
+          consensus=false
         fi
       fi
-      if [ \${concensus} == false ]
+      if [ \${consensus} == false ]
       then
         seqtypeError=true
         seqtypeError_details=\$(echo "**Infered species confidence is low:**\\n")
@@ -901,7 +903,16 @@ process seqwho {
       speciesError=false
       echo -e "LOG: species matches: Submitted=${speciesMeta}; Inferred=\${speciesInfer}" >> ${repRID}.seqwho.log
     fi
+
+    # save seqwho multiqc report
+    echo -e "Read\tSeq Type\tSpecies\tConfidence\tSeq Type Confidence\tSeq Type Consensus\tSpecies Confidence" > seqwhoInfer.tsv
+    echo -e "Read 1\y\${seqtypeR1}\t\${speciesR1}\t\${confidenceR1}\${seqtypeConfidenceR1}\t\${consensus}\t\${speciesConfidenceR1}" >> seqwhoInfer.tsv
+    if [ "${ends}" == "pe" ]
+    then
+      echo -e "Read 2\y\${seqtypeR2}\t\${speciesR2}\t\${confidenceR2}\${seqtypeConfidenceR2}\t\${consensus}\t\${speciesConfidenceR2}" >> seqwhoInfer.tsv
+    fi
     
+
     # save species file
     echo "\${speciesInfer}" > inferSpecies.csv
 
@@ -2008,6 +2019,7 @@ process aggrQC {
   input:
     path multiqcConfig
     path bicfLogo
+    path seqwhoInfer
     path softwareReferences
     path softwareVersions
     path fastqc
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index ed1375a..fdcdcca 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -37,10 +37,10 @@ top_modules:
       name: 'Count'
       info: 'Replicate Feature Count QC Results'
   - hisat2:
-      name: 'Inference: Align'
+      name: 'Inference: Spike-in'
       info: 'Inference Alignment (1M downsampled reads) QC Results'
       path_filters:
-        - '*alignSampleSummary*'
+        - 'ERCC.alignSampleSummary*'
   - rseqc:
       name: 'Inference: Stranded'
       info: '1M Downsampled Reads Strandedness Inference Results'
@@ -166,6 +166,30 @@ custom_data:
             71 - 80
             81 - 90
             91 - 100
+    seqwho:
+        file_format: 'tsv'
+        section_name: 'Inference: Sequencing Type & Species'
+        description: 'This is the inference results from the SeqWho tool'
+        plot_type: 'table'
+        pconfig:
+            id: 'ref'
+            scale: false
+            format: '{}'
+        headers:
+            Read:
+                description: 'Sequencing read (R1/R2)'
+            Seq Type:
+                description: 'Inferred Sequence Type'
+            Species:
+                description: 'Inferred Species'
+            Confidence:
+                description: 'Call confidence'
+            Seq Type Confidence:
+                description: 'Seqence type call confidence (1=high, 0=low)'
+            Seq Type Consensus:
+                description: 'Low confidence sequence type call sampling inference consensus'
+            Species Confidence:
+                description: 'Species call confidence (1=high, 0=low)'
 
 sp:
     run:
@@ -178,3 +202,5 @@ sp:
         fn: 'reference.tsv'
     tin:
         fn: '*_tin.hist.tsv'
+    seqwho:
+	fn: 'seqwhoInfer.tsv'
-- 
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