From c0a39ab89165e3ae8942f6b0a858e2eee8bca15e Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 13 Nov 2020 20:27:26 -0600
Subject: [PATCH] Update changes to reflect only the change in order of steps.
 Fix output files.

---
 CHANGELOG.md        | 2 +-
 workflow/rna-seq.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 02c9891..57b9544 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +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
-* Added back parallel form of trim_galore and now use fastqc after trim step
+* 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
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index aa6e8a1..f12ec9b 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -341,7 +341,7 @@ process trimData {
 
   output:
     path ("*.fq.gz") into fastqsTrim
-    path ("*.fastq.gz") into fastqs_fastqc
+    path ("*.fastq.gz") includeInput:true into fastqs_fastqc
     path ("*_trimming_report.txt") into trimQC
     path ("readLength.csv") into inferMetadata_readLength
 
@@ -881,7 +881,7 @@ process alignData {
 }
 
 // Replicate rawBam for multiple process inputs
-rawBam.set {
+rawBam.into {
   rawBam_dedupData
 }
 
-- 
GitLab