From 6269b5affbf317e10cc1f37d8a48928607450fda Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 6 Jan 2021 20:37:47 -0600
Subject: [PATCH] Fix species error variable
---
workflow/conf/Replicate_For_Input_Bag.json | 2 +-
workflow/rna-seq.nf | 30 +++++++++++-----------
workflow/scripts/bdbag_fetch.sh | 17 +++++++++++-
3 files changed, 32 insertions(+), 17 deletions(-)
diff --git a/workflow/conf/Replicate_For_Input_Bag.json b/workflow/conf/Replicate_For_Input_Bag.json
index 4380e46..278d0bf 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)/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/url:=URI,length:=File_size,filename:=File_Name,md5:=MD5,Study_RID,Experiment_RID,Replicate_RID?limit=none"
}
}
]
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 7d439ec..95239b0 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -945,21 +945,21 @@ speciesError_fl.splitCsv(sep: ",", header: false).separate(
)
// Replicate errors for multiple process inputs
-fastqCountError.into {
- fastqCountError_checkMetadata
- fastqCountError_uploadExecutionRun
- fastqCountError_getRef
- fastqCountError_alignData
- fastqCountError_dedupData
- fastqCountError_makeBigWig
- fastqCountError_countData
- fastqCountError_fastqc
- fastqCountError_dataQC
- fastqCountError_aggrQC
- fastqCountError_uploadQC
- fastqCountError_uploadProcessedFile
- fastqCountError_uploadOutputBag
- fastqCountError_failPreExecutionRun
+speciesError.into {
+ speciesError_checkMetadata
+ speciesError_uploadExecutionRun
+ speciesError_getRef
+ speciesError_alignData
+ speciesError_dedupData
+ speciesError_makeBigWig
+ speciesError_countData
+ speciesError_fastqc
+ speciesError_dataQC
+ speciesError_aggrQC
+ speciesError_uploadQC
+ speciesError_uploadProcessedFile
+ speciesError_uploadOutputBag
+ speciesError_failPreExecutionRun
}
/*
diff --git a/workflow/scripts/bdbag_fetch.sh b/workflow/scripts/bdbag_fetch.sh
index d805f67..f3f5405 100644
--- a/workflow/scripts/bdbag_fetch.sh
+++ b/workflow/scripts/bdbag_fetch.sh
@@ -10,5 +10,20 @@ then
done
elif [ "${3}" == "TEST" ]
then
- bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1} --debug
+ bdbag --materialize ${1} --debug
+ validateError=true
+ bdbag --validate full ${1} && validateError=false
+ if validateError
+ then
+ n=0
+ until [ "${n}" -ge "3" ]
+ do
+ bdbag --resolve-fetch missing --validate full ${1} --debug && validateError=false && break
+ n=$((n+1))
+ sleep 15
+ done
+ fi
+ if validateError
+ then
+ exit 1
fi
--
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