Merge branch '65-trim_galore' into 'develop'

Add back parallel trim step. Moved fastqc step after trim.

Closes #65

See merge request !50

CHANGELOG.md

@@ -9,6 +9,7 @@
 * Make pull references from BioHPC default (including in biohpc.config)
 * Start using new gudmaprbk dockerhub (images autobuilt)
 * Moved consistency checks to be fully python
+* Changed order of steps so that fastqc is done after the trim step
 
 *Known Bugs*
 * Datahub reference pull uses dev.gudmap.org as source until referencencs are placed on production

workflow/rna-seq.nf

@@ -227,14 +227,12 @@ if (fastqsForce != "") {
   Channel
     .fromPath(fastqsForce)
     .ifEmpty { exit 1, "override inputBag file not found: ${fastqsForce}" }
-    .collect().into {
+    .collect().set {
       fastqs_trimData
-      fastqs_fastqc
     }
 } else {
-  fastqs.into {
+  fastqs.set {
     fastqs_trimData
-    fastqs_fastqc
   }
 }
 
@@ -343,6 +341,7 @@ process trimData {
 
   output:
     path ("*.fq.gz") into fastqsTrim
+    path ("*.fastq.gz", includeInputs:true) into fastqs_fastqc
     path ("*_trimming_report.txt") into trimQC
     path ("readLength.csv") into inferMetadata_readLength