From bee831eae744ab6952fc63e1ab9928e5dec58902 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 5 Jan 2021 17:25:33 -0600
Subject: [PATCH] Fix combines with new errors
---
workflow/rna-seq.nf | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 37ceb40..fcae526 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -575,7 +575,7 @@ fastqsTrim.into {
}
// Combine inputs of getRefInfer
-getRefInferInput = referenceInfer.combine(deriva_getRefInfer.combine(script_refDataInfer))
+getRefInferInput = referenceInfer.combine(deriva_getRefInfer.combine(script_refDataInfer.combine(fastqCountError_getRefInfer.combine(fastqReadError_getRefInfer))))
/*
* getRefInfer: dowloads appropriate reference for metadata inference
@@ -584,17 +584,15 @@ process getRefInfer {
tag "${refName}"
input:
- tuple val (refName), path (credential, stageAs: "credential.json"), path (script_refDataInfer) from getRefInferInput
- val fastqCountError_getRefInfer
- val fastqReadError_getRefInfer
+ tuple val (refName), path (credential, stageAs: "credential.json"), path (script_refDataInfer), val (fastqCountError), val (fastqReadError) from getRefInferInput
output:
tuple val (refName), path ("hisat2", type: 'dir'), path ("*.fna"), path ("*.gtf") into refInfer
path ("${refName}", type: 'dir') into bedInfer
when:
- fastqCountError_getRefInfer == "false"
- fastqReadError_getRefInfer == "false"
+ fastqCountError == "false"
+ fastqReadError == "false"
script:
"""
@@ -602,10 +600,10 @@ process getRefInfer {
ulimit -a >> ${repRID}.${refName}.getRefInfer.log
# link credential file for authentication
- echo -e "LOG: linking deriva credentials" >> ${repRID}.getRefInfer.log
+ echo -e "LOG: linking deriva credentials" >> ${repRID}.${refName}.getRefInfer.log
mkdir -p ~/.deriva
ln -sf `readlink -e credential.json` ~/.deriva/credential.json
- echo -e "LOG: linked" >> ${repRID}.getRefInfer.log
+ echo -e "LOG: linked" >> ${repRID}.${refName}.getRefInfer.log
# set the reference name
if [ "${refName}" == "ERCC" ]
--
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