From e5fdb858513531962675e9b0783dcf5f410a40b9 Mon Sep 17 00:00:00 2001
From: Gervaise Henry <GHENRY@swmed.org>
Date: Sat, 14 Mar 2020 20:28:41 -0500
Subject: [PATCH] Removed unused script
---
workflow/rna-seq.nf | 2 --
workflow/scripts/aggregateInference.R | 43 ---------------------------
2 files changed, 45 deletions(-)
delete mode 100644 workflow/scripts/aggregateInference.R
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 7fcc2fd..32cf5a8 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -39,7 +39,6 @@ referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references"
script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbagFetch.sh")
script_parseMeta = Channel.fromPath("${baseDir}/scripts/parseMeta.py")
script_inferMeta = Channel.fromPath("${baseDir}/scripts/inferMeta.sh")
-script_aggregateInference = Channel.fromPath("${baseDir}/scripts/aggregateInference.R")
/*
* splitData: split bdbag files by replicate so fetch can occure in parallel, and rename files to replicate rid
@@ -423,7 +422,6 @@ process inferMetadata {
input:
path script_inferMeta
- path script_aggregateInference
path reference_inferMeta
set val (repRID), path (inBam), path (inBai) from rawBam_inferMetadata
diff --git a/workflow/scripts/aggregateInference.R b/workflow/scripts/aggregateInference.R
deleted file mode 100644
index 3e8388d..0000000
--- a/workflow/scripts/aggregateInference.R
+++ /dev/null
@@ -1,43 +0,0 @@
-gc()
-library(optparse)
-
-option_list=list(
- make_option("--endness",action="store",type='character',help="Infered Endness"),
- make_option("--stranded",action="store",type='character',help="Infered Strandedness"),
- make_option("--strategy",action="store",type='character',help="Infered Sequencing Strategy"),
- make_option("--percentF",action="store",type='double',help="Percent Forward Aligned Reads"),
- make_option("--percentR",action="store",type='double',help="Percent Reverse Aligned Reads"),
- make_option("--percentFail",action="store",type='double',help="Percent Failed Aligned Reads"),
- make_option("--tin",action="store",type='character',help="TIN File")
-)
-opt=parse_args(OptionParser(option_list=option_list))
-rm(option_list)
-
-if (length(setdiff(c("endness","stranded","strategy","percentF","percentR","percentFail","tin","help"),names(opt))) != 0){
- stop(paste0("No input missing ",setdiff(c("endness","stranded","strategy","percentF","percentR","percentFail","tin","help"),names(opt)),", exiting."))
-} else if (!file.exists(opt$tin)){
- stop("No tin file passed, exiting.")
-}
-
-if (opt$endness == "PairEnd"){
- endness <- "pe"
-} else if (opt$endness == "SingleEnd"){
- endness <- "se"
-}
-
-percentF <- round(opt$percentF,digits=2)
-percentR <- round(opt$percentR,digits=2)
-percentFail <- round(opt$percentFail,digits=2)
-
-repRID <- basename(gsub(".sorted.deduped.tin.xls","",opt$tin))
-
-tin <- read.delim(opt$tin,sep="\t")
-
-tin.min <- round(min(tin$TIN),digits=2)
-tin.med <- round(median(tin$TIN),digits=2)
-tin.max <- round(max(tin$TIN),digits=2)
-tin.sd <- round(sd(tin$TIN),digits=2)
-
-output <- paste(endness,opt$stranded,opt$strategy,percentF,percentR,percentFail,tin.min,tin.med,tin.max,tin.sd,sep=",")
-
-write(output,file="infer.csv")
--
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