From f6ee4fbe9c691f977a02c983b05340e79b14b1cd Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 6 Jan 2021 09:51:22 -0600
Subject: [PATCH] Fix align sample combine
---
workflow/rna-seq.nf | 10 ++++------
1 file changed, 4 insertions(+), 6 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index fcae526..1244881 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -701,7 +701,7 @@ process downsampleData {
}
// Replicate the dowsampled fastq's and attatched to the references
-inferInput = endsManual_alignSampleData.combine(refInfer.combine(fastqs1Sample.collect().combine(fastqs2Sample.collect())))
+inferInput = endsManual_alignSampleData.combine(refInfer.combine(fastqs1Sample.collect().combine(fastqs2Sample.collect().combine(fastqCountError_alignSampleData.combine(val fastqReadError_alignSampleData)))))
/*
* alignSampleData: aligns the downsampled reads to a reference database
@@ -710,9 +710,7 @@ process alignSampleData {
tag "${ref}"
input:
- tuple val (ends), val (ref), path (hisat2), path (fna), path (gtf), path (fastq1), path (fastq2) from inferInput
- val fastqCountError_alignSampleData
- val fastqReadError_alignSampleData
+ tuple val (ends), val (ref), path (hisat2), path (fna), path (gtf), path (fastq1), path (fastq2), val (fastqCountError), val (fastqReadError) from inferInput
output:
path ("${ref}.sampled.sorted.bam") into sampleBam
@@ -720,8 +718,8 @@ process alignSampleData {
path ("${ref}.alignSampleSummary.txt") into alignSampleQC
when:
- fastqCountError_alignSampleData == "false"
- fastqReadError_alignSampleData == "false"
+ fastqCountError == "false"
+ fastqReadError == "false"
script:
"""
--
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