From 710cb79676d11663c8d951373265c9c80325aee3 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 11 Aug 2020 14:14:55 +0200
Subject: [PATCH] Fix index localization.
---
CHANGELOG.md | 2 ++
bam2fastx.wdl | 14 ++++++++++++--
2 files changed, 14 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 272499c..af61315 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
++ Add copy command to bam2fastx tasks to make sure bam file and its index are
+ always in the same directory.
+ Add wdl file for pacbio's bam2fastx tool.
version 4.0.0
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 5e5fb50..6a09202 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -24,6 +24,7 @@ task Bam2Fasta {
input {
File inputFile
File bamIndex
+ String basenameInputFile = basename(inputFile)
String outputPrefix
Int compressionLevel = 1
Boolean splitByBarcode = false
@@ -38,12 +39,16 @@ task Bam2Fasta {
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
+ # The bam file and its index need to be in the same directory.
+ # Cromwell will put them in separate iputs folders.
+ cp ~{inputFile} ./
+ cp ~{bamIndex} ./
bam2fasta \
--output ~{outputPrefix} \
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ~{inputFile}
+ ./~{basenameInputFile}
}
output {
@@ -76,6 +81,7 @@ task Bam2Fasta {
task Bam2Fastq {
input {
File inputFile
+ String basenameInputFile = basename(inputFile)
File bamIndex
String outputPrefix
Int compressionLevel = 1
@@ -91,12 +97,16 @@ task Bam2Fastq {
command {
set -e
mkdir -p "$(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} \
- ~{inputFile}
+ ./~{basenameInputFile}
}
output {
--
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