From ac21c8213fc5b7cf75e4f1d79afc42b439e4f045 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 12 Mar 2020 20:00:59 -0500
Subject: [PATCH] Remove R aggregation
---
workflow/rna-seq.nf | 31 ++++---------------------------
1 file changed, 4 insertions(+), 27 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 15e8eff..0a56dd9 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -421,7 +421,8 @@ process inferMetadata {
set val (repRID), path (inBam), path (inBai) from dedupBam_rseqc
output:
- path "infer.csv" into inferMetadata
+ path "infer.csv" into inferedMetadata
+ path "${inBam.baseName}.tin.xls" into tin
script:
@@ -470,31 +471,7 @@ process inferMetadata {
# calcualte TIN values per feature
tin.py -i "${inBam}" -r ./bed/genome.bed
- # aggregate infered metadata (including generate TIN stats)
- Rscript aggregateInference.R --endness "\${endness}" --stranded "\${stranded}" --strategy "\${strategy}" --percentF \${percentF} --percentR \${percentR} --percentFail \${fail} --tin "${inBam.baseName}.tin.xls"
+ # write infered metadata to file
+ echo \${endness},\${stranded},\${strategy},\${percentF},\${percentR},\${percentFail} > infer.csv
"""
}
-
-// Split infered metadata into separate channels
-endsMetaI = Channel.create()
-strandedI = Channel.create()
-strategyI = Channel.create()
-percentFI = Channel.create()
-percentRI = Channel.create()
-percentFailI = Channel.create()
-tinMinI = Channel.create()
-tinMedI = Channel.create()
-tinMaxI = Channel.create()
-tinSDI = Channel.create()
-inferMetadata.splitCsv(sep: ",", header: false).separate(
- endsMetaI,
- strandedI,
- strategyI,
- percentFI,
- percentRI,
- percentFailI,
- tinMinI,
- tinMedI,
- tinMaxI,
- tinSDI
-)
--
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