From 4204877339d65a0e54cfa304014239effec320bf Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 13 Sep 2020 21:19:55 -0500
Subject: [PATCH] Add extractRefData.py as channel
---
workflow/rna-seq.nf | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 41e11c7..ba0d832 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -71,10 +71,13 @@ bicfLogo = Channel.fromPath("${baseDir}/../docs/bicf_logo.png")
script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbagFetch.sh")
script_parseMeta = Channel.fromPath("${baseDir}/scripts/parseMeta.py")
script_inferMeta = Channel.fromPath("${baseDir}/scripts/inferMeta.sh")
+script_refDataInfer = Channel.fromPath("${baseDir}/scripts/extractRefData.py")
+script_refData = Channel.fromPath("${baseDir}/scripts/extractRefData.py")
script_calculateTPM = Channel.fromPath("${baseDir}/scripts/calculateTPM.R")
script_convertGeneSymbols = Channel.fromPath("${baseDir}/scripts/convertGeneSymbols.R")
script_tinHist = Channel.fromPath("${baseDir}/scripts/tinHist.py")
+
/*
* trackStart: track start of pipeline
*/
@@ -381,6 +384,7 @@ process getRefInfer {
input:
path credential, stageAs: "credential.json" from deriva_getRefInfer
+ path script_refDataInfer
val refName from referenceInfer
output:
@@ -710,6 +714,7 @@ process getRef {
input:
path credential, stageAs: "credential.json" from deriva_getRef
+ path script_refData
val spike from spikeInfer_getRef
val species from speciesInfer_getRef
--
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