From d9be943ed7dd6dbbeeddf112ea5248fbfa1da97f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 1 Mar 2021 22:45:58 -0600
Subject: [PATCH] Add missing speciesError to when
---
rna-seq.nf | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 186a895..52c2a3f 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -981,24 +981,25 @@ speciesErrorSeqwho.into {
speciesErrorSeqwho_uploadQC_fail
}
speciesError.into {
- speciesError_checkMetadata
- speciesError_uploadExecutionRun
+ speciesError_trimData
speciesError_getRef
+ speciesError_downsampleData
+ speciesError_alignSampleDataERCC
speciesError_alignSampleData
speciesError_inferMetadata
+ speciesError_checkMetadata
speciesError_alignData
speciesError_dedupData
speciesError_makeBigWig
speciesError_countData
- speciesError_fastqc
speciesError_dataQC
speciesError_aggrQC
+ speciesError_uploadExecutionRun
speciesError_uploadQC
- speciesError_uploadQC_fail
speciesError_uploadProcessedFile
speciesError_uploadOutputBag
speciesError_finalizeExecutionRun
- speciesError_failPreExecutionRun_species
+ speciesError_uploadQC_fail
}
/*
@@ -1073,6 +1074,7 @@ process trimData {
val fastqFileError from fastqFileError_trimData
val seqtypeError from seqtypeError_trimData
val speciesErrorSeqwho from speciesErrorSeqwho_trimData
+ val speciesError from speciesError_trimData
output:
path ("*.fq.gz") into fastqsTrim
@@ -1080,7 +1082,7 @@ process trimData {
path ("readLength.csv") into readLengthInfer_fl
when:
- fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false"
script:
"""
@@ -1136,12 +1138,13 @@ process downsampleData {
val fastqFileError from fastqFileError_downsampleData
val seqtypeError from seqtypeError_downsampleData
val speciesErrorSeqwho from speciesErrorSeqwho_downsampleData
+ val speciesError from speciesError_downsampleData
output:
path ("sampled.{1,2}.fq") into fastqsSample
when:
- fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false"
script:
"""
@@ -1186,13 +1189,14 @@ process alignSampleDataERCC {
val fastqFileError from fastqFileError_alignSampleDataERCC
val seqtypeError from seqtypeError_alignSampleDataERCC
val speciesErrorSeqwho from speciesErrorSeqwho_alignSampleDataERCC
+ val speciesError from speciesError_alignSampleDataERCC
output:
path "inferSpike.csv" into inferSpike_fl
path ("ERCC.alignSampleSummary.txt") into alignSampleQC_ERCC
when:
- fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesError == "false"
script:
"""
--
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