From 01df29baef579cce73a32cd109d5405d45c197bd Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 11 Aug 2020 15:18:17 +0200
Subject: [PATCH] Change lima outputs.
---
CHANGELOG.md | 3 +--
bam2fastx.wdl | 14 ++------------
lima.wdl | 9 ++++++---
3 files changed, 9 insertions(+), 17 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b839b35..57bbfec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,8 +11,7 @@ that users understand how the changes affect the new version.
version 4.1.0-dev
---------------------------
-+ Add copy command to bam2fastx tasks to make sure bam file and its index are
- always in the same directory.
++ Remove globs from lima outputs.
+ Added a task for GRIDSS.
+ Add wdl file for pacbio's bam2fastx tool.
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 6a09202..5e5fb50 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -24,7 +24,6 @@ task Bam2Fasta {
input {
File inputFile
File bamIndex
- String basenameInputFile = basename(inputFile)
String outputPrefix
Int compressionLevel = 1
Boolean splitByBarcode = false
@@ -39,16 +38,12 @@ task Bam2Fasta {
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
- # The bam file and its index need to be in the same directory.
- # Cromwell will put them in separate iputs folders.
- cp ~{inputFile} ./
- cp ~{bamIndex} ./
bam2fasta \
--output ~{outputPrefix} \
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ./~{basenameInputFile}
+ ~{inputFile}
}
output {
@@ -81,7 +76,6 @@ task Bam2Fasta {
task Bam2Fastq {
input {
File inputFile
- String basenameInputFile = basename(inputFile)
File bamIndex
String outputPrefix
Int compressionLevel = 1
@@ -97,16 +91,12 @@ task Bam2Fastq {
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
- # The bam file and its index need to be in the same directory.
- # Cromwell will put them in separate iputs folders.
- cp ~{inputFile} ./
- cp ~{bamIndex} ./
bam2fastq \
--output ~{outputPrefix} \
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ./~{basenameInputFile}
+ ~{inputFile}
}
output {
diff --git a/lima.wdl b/lima.wdl
index 2e8a708..1a40b1c 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -95,12 +95,15 @@ task Lima {
cp "~{basename(outputPrefix)}.fl.lima.counts" "~{outputPrefix}.fl.lima.counts"
cp "~{basename(outputPrefix)}.fl.lima.report" "~{outputPrefix}.fl.lima.report"
cp "~{basename(outputPrefix)}.fl.lima.summary" "~{outputPrefix}.fl.lima.summary"
+ find . -path "*.bam" > bamFiles.txt
+ find . -path "*.bam.pbi" > bamIndexes.txt
+ find . -path "*.subreadset.xml" > subreadsets.txt
}
output {
- Array[File] limaBam = glob("*.bam")
- Array[File] limaBamIndex = glob("*.bam.pbi")
- Array[File] limaXml = glob("*.subreadset.xml")
+ Array[File] limaBam = read_lines("bamFiles.txt")
+ Array[File] limaBamIndex = read_lines("bamIndexes.txt")
+ Array[File] limaXml = read_lines("subreadsets.txt")
File limaStderr = outputPrefix + ".fl.stderr.log"
File limaJson = outputPrefix + ".fl.json"
File limaCounts = outputPrefix + ".fl.lima.counts"
--
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