Commit 4f879f72 authored by Boom's avatar Boom
Browse files

Try to adjust localization.

parent 833ad0bf
......@@ -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.
......
......@@ -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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