From 4f879f72aec90d36d0201e9c1b54154f9decb757 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 14 Jun 2021 12:40:32 +0200
Subject: [PATCH] Try to adjust localization.
---
CHANGELOG.md | 7 ++++++-
bam2fastx.wdl | 12 ++++++------
2 files changed, 12 insertions(+), 7 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 83da539..11a92d8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,12 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
-+ Fix output files in ccs.wdl.
++ Change the way localization of the input bam files and index are handled
+ in the bam2fastx tasks.
++ Add new parameters from CCS version 6.0.0 and add two new outputs:
+ `ccs_report.txt` & `zmw_metrics.json.gz`.
++ Change CutAdapt memory to `5G`.
++ Increase multiqc base time from 5 to 10.
+ Update biowdl-input-converter to version 0.3.
+ Update minimap2 to version 2.20.
+ Update lima to version 2.2.0.
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 0bdccca..4a2ecf8 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -44,13 +44,13 @@ task Bam2Fasta {
bamFiles=""
for bamFile in ~{sep=" " bam}
do
- ln $bamFile .
- bamFiles=$bamFiles" $(basename $bamFile)"
+ cp $bamFile ./
+ bamFiles=$bamFiles" ./$(basename $bamFile)"
done
for index in ~{sep=" " bamIndex}
do
- ln $index .
+ cp $index ./
done
bam2fasta \
@@ -112,13 +112,13 @@ task Bam2Fastq {
bamFiles=""
for bamFile in ~{sep=" " bam}
do
- ln $bamFile .
- bamFiles=$bamFiles" $(basename $bamFile)"
+ cp $bamFile ./
+ bamFiles=$bamFiles" ./$(basename $bamFile)"
done
for index in ~{sep=" " bamIndex}
do
- ln $index .
+ cp $index ./
done
bam2fastq \
--
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