Fix seqwho tsv output for multiqc

rna-seq.nf

@@ -919,11 +919,11 @@ process seqwho {
     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\t\${seqtypeR1}\t\${speciesR1}\t\${confidenceR1}\${seqtypeConfidenceR1}\t\${consensus}\t\${speciesConfidenceR1}" >> seqwhoInfer.tsv
+    echo -e "Read\tSeq Type\tSpecies\tSeq Type Confidence\tSeq Type Consensus\tSpecies Confidence" > seqwhoInfer.tsv
+    echo -e "Read 1\t\${seqtypeR1}\t\${speciesR1}\t\${seqtypeConfidenceR1}\t\${consensus}\t\${speciesConfidenceR1}" >> seqwhoInfer.tsv
     if [ "${ends}" == "pe" ]
     then
-      echo -e "Read 2\t\${seqtypeR2}\t\${speciesR2}\t\${confidenceR2}\${seqtypeConfidenceR2}\t\${consensus}\t\${speciesConfidenceR2}" >> seqwhoInfer.tsv
+      echo -e "Read 2\t\${seqtypeR2}\t\${speciesR2}\t\t\${seqtypeConfidenceR2}\t\${consensus}\t\${speciesConfidenceR2}" >> seqwhoInfer.tsv
     fi
     
 

workflow/conf/multiqc_config.yaml

@@ -182,14 +182,12 @@ custom_data:
                 description: 'Inferred Sequence Type'
             Species:
                 description: 'Inferred Species'
-            Confidence:
-                description: 'Call confidence'
             Seq Type Confidence:
-                description: 'Seqence type call confidence (1=high, 0=low)'
+                description: 'Seqence type call confidence'
             Seq Type Consensus:
                 description: 'Low confidence sequence type call sampling inference consensus'
             Species Confidence:
-                description: 'Species call confidence (1=high, 0=low)'
+                description: 'Species call confidence'
 
 sp:
     run: