From 5d9c691f9fabf1c4963ae74bf0c4e4e71b6a5c1d Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 19 Jan 2021 19:30:50 -0600
Subject: [PATCH] Filter input bag export config to only get fastq's matching
convention
---
CHANGELOG.md | 1 +
workflow/conf/Replicate_For_Input_Bag.json | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58b5bff..d35003f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@
* Move fastqc process before trim to catch fastq errors (#107)
* Only use fastq's that match *.R[1,2].fastq.gz naming convention (#107)
* Add error output for no fastq's
+* Update input bag export config to only fetch fastq's that match *.R[1,2].fastq.gz naming convention
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
diff --git a/workflow/conf/Replicate_For_Input_Bag.json b/workflow/conf/Replicate_For_Input_Bag.json
index 278d0bf..842cf62 100644
--- a/workflow/conf/Replicate_For_Input_Bag.json
+++ b/workflow/conf/Replicate_For_Input_Bag.json
@@ -89,7 +89,7 @@
"processor": "fetch",
"processor_params": {
"output_path": "assets/Study/{Study_RID}/Experiment/{Experiment_RID}/Replicate/{Replicate_RID}",
- "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(RID)=(RNASeq:File:Replicate_RID)/File_Type=FastQ/url:=URI,length:=File_size,filename:=File_Name,md5:=MD5,Study_RID,Experiment_RID,Replicate_RID?limit=none"
+ "query_path": "/attribute/M:=RNASeq:Replicate/RID={rid}/(RID)=(RNASeq:File:Replicate_RID)/File_Type=FastQ/File_Name::ciregexp::%5B_.%5DR%5B12%5D%5C.fastq%5C.gz/url:=URI,length:=File_size,filename:=File_Name,md5:=MD5,Study_RID,Experiment_RID,Replicate_RID?limit=none"
}
}
]
--
GitLab