From 445f6693dada7e062b18f83d90fd0848968c0fb9 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 25 Jul 2021 16:34:07 -0500
Subject: [PATCH] Change seqwho ref location
---
CHANGELOG.md | 2 ++
rna-seq.nf | 5 ++++-
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4a27c94..6e07862 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
# v.2.0.1 (indev)
**User Facing**
* Corrected spelling of inferred (#125)
+* Add param for seqwho reference (#127)
**Background**
* Corrected file search parameters due to name inconsistency (#129)
@@ -11,6 +12,7 @@
* Remove "fail" integration CI tests (#133 addendum)
* Add licence header to nf file, R and python scriptsand pytest scripts
* Stop using RCB and RMB (default) with deriva.core insert calls to match server update (#134)
+* Replace default seqwho reference location to one provided by source lab (#127)
# v2.0.0
**User Facing**
diff --git a/rna-seq.nf b/rna-seq.nf
index 604fdaf..f7875eb 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -23,6 +23,7 @@ params.source = "dev"
params.refMoVersion = "38.p6.vM25"
params.refHuVersion = "38.p13.v36"
params.refERCCVersion = "92"
+params.seqwhoRef = "https://cloud.biohpc.swmed.edu/index.php/s/sP48taKmymSkJBM/download"
params.outDir = "${baseDir}/output"
params.upload = false
params.email = ""
@@ -67,6 +68,7 @@ repRID = params.repRID
refMoVersion = params.refMoVersion
refHuVersion = params.refHuVersion
refERCCVersion = params.refERCCVersion
+seqwhoRef = params.seqwhoRef
outDir = params.outDir
logsDir = "${outDir}/Logs"
upload = params.upload
@@ -714,6 +716,7 @@ process seqwho {
tag "${repRID}"
input:
+ val seqwhoRef
path (fastq) from fastqs_seqwho
val ends from endsManual_seqwho
val speciesMeta from speciesMeta_seqwho
@@ -734,7 +737,7 @@ process seqwho {
ulimit -a >> ${repRID}.seqwho.log
# get seqwho index
- wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download
+ wget -O SeqWho.ix ${seqwhoRef}
echo -e "LOG: seqwho index downloaded" >> ${repRID}.seqwho.log
# run seqwho
--
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