From 2fa11a2c95bc0e3a1c0b4a7c493449208e81f151 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 10 Sep 2019 16:27:37 +0200
Subject: [PATCH] remove deprecayed tasks
---
CHANGELOG.md | 4 +++
bioconda.wdl | 30 --------------------
mergecounts.wdl | 75 -------------------------------------------------
3 files changed, 4 insertions(+), 105 deletions(-)
delete mode 100644 bioconda.wdl
delete mode 100644 mergecounts.wdl
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7025e17..cf3f28a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,10 @@ that users understand how the changes affect the new version.
version 1.0.0-dev
---------------------------
++ Removed deprecated tasks:
+ + bioconda.installPrefix
+ + mergecounts.MergeCounts
++ GATK.BaseRecalibrator: "knownIndelsSitesVCFs" and "knownIndelsSitesVCFIndexes" are no longer optional, but now have a default of "[]"
+ Removed BWA index task
+ Removed unused "picardJar" input from bwa.wdl
+ All inputs to bedtools Sort are now reflected in the generated command
diff --git a/bioconda.wdl b/bioconda.wdl
deleted file mode 100644
index 0a513dd..0000000
--- a/bioconda.wdl
+++ /dev/null
@@ -1,30 +0,0 @@
-version 1.0
-# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2017
-
-# Bioconda installs
-
-task installPrefix {
- input {
- Array[String] requirements
- String prefix
- String condaPath = "conda"
- }
-
- command <<<
- ~{condaPath} create \
- --json -q \
- --yes \
- --override-channels \
- --channel bioconda \
- --channel conda-forge \
- --channel defaults \
- --channel r \
- --prefix ${prefix} \
- ~{sep=' ' requirements}
- >>>
-
- output {
- File condaEnvPath=prefix
- File condaJson=stdout()
- }
- }
diff --git a/mergecounts.wdl b/mergecounts.wdl
deleted file mode 100644
index e89a39e..0000000
--- a/mergecounts.wdl
+++ /dev/null
@@ -1,75 +0,0 @@
-version 1.0
-
-#DEPRECATED
-task MergeCounts {
- input {
- Array[File] inputFiles
- String outputFile
- Int featureColumn
- Int valueColumn
- Boolean inputHasHeader
- String featureAttribute = "gene_id"
- File referenceGtf
- Array[String]+? additionalAttributes
-
- Int? memoryPerSample = 3
- }
-
- # Based on a script by Szymon Kielbasa/Ioannis Moustakas
- command <<<
- set -e
- mkdir -p ~{sub(outputFile, basename(outputFile) + "$", "")}
- R --no-save <<CODE
- Sys.setlocale("LC_ALL","English") #FIXME this should be set in the docker image instead
-
- library(dplyr)
- library(reshape2)
- library(refGenome)
-
- list.of.files <- c("~{sep='", "' inputFiles}")
-
- value.i <- ~{valueColumn}
- feature.i <- ~{featureColumn}
- header <- ~{true="TRUE" false="FALSE" inputHasHeader}
- feature.attribute <- "~{featureAttribute}"
- additional.attributes <- c(~{true='"' false="" defined(additionalAttributes)}~{sep='", "' additionalAttributes}~{true='"' false="" defined(additionalAttributes)})
- reference.gtf <- "~{referenceGtf}"
- output.path <- "~{outputFile}"
-
- d <- do.call(rbind, lapply(list.of.files, function(file){
- d <- read.table(file, sep="\t", header=header, comment.char="#")
-
- filename <- basename(file)
- colnames(d)[value.i] <- sub("\\\.[^\\\.]*\$", "", filename)
- colnames(d)[feature.i] <- "feature"
-
- d <- d %>% melt(id.vars=feature.i, variable.name="sample",
- value.name="count")
- }))
-
- d <- d %>% dcast(feature ~ sample, value.var="count")
-
- gtf <- ensemblGenome(dirname(reference.gtf))
- read.gtf(gtf, basename(reference.gtf))
-
- gtf.table <- gtf@ev\$gtf
- gtf.table <- gtf.table[order(gtf.table[,feature.attribute]),]
- gtf.table <- gtf.table[!duplicated(gtf.table[,feature.attribute]),]
- id.table <- gtf.table[, c(feature.attribute, additional.attributes), drop=F]
- output.table <- merge(id.table, d, all.y = T, by.y="feature",
- by.x=feature.attribute)
-
- write.table(output.table, file=output.path, sep="\t", quote=FALSE,
- row.names=FALSE, na="")
- CODE
- >>>
-
- output {
- File mergedCounts = outputFile
- }
-
- runtime {
- memory: 4 + (memoryPerSample * length(inputFiles))
- docker: "biowdl/mergecounts:1.0"
- }
-}
\ No newline at end of file
--
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