From 2eddbd49123615a1e43cc15a5a35bce1136eea42 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 18 Oct 2017 09:31:26 -0500
Subject: [PATCH] Fix output dedupdesign.
---
workflow/main.nf | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 636cb53..e485386 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -164,8 +164,10 @@ process filterReads {
}
// Define channel collecting new design file
-dedupDesign = dedupReads.
- collectFile(name:'design_dedup.tsv', seed:"sample_id\tbam_reads\tbam_index\tbiosample\tfactor\ttreatment\treplicate\tcontrolId\n", storeDir:"$baseDir/output/design")
+dedupDesign = dedupReads
+ .map{ sampleId, bam, bai, biosample, factor, treatment, replicate, controlId ->
+ "$sample_id\t$bam\t$bai\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
+ .collectFile(name:'design_dedup.tsv', seed:"sample_id\tbam_reads\tbam_index\tbiosample\tfactor\ttreatment\treplicate\tcontrolId\n", storeDir:"$baseDir/output/design")
// Quality Metrics using deeptools
process experimentQC {
--
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