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biowdl
tasks
Commits
f111c363
Commit
f111c363
authored
4 years ago
by
JasperBoom
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CHANGELOG.md
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-8
5 additions, 8 deletions
CHANGELOG.md
README.md
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README.md
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CHANGELOG.md
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f111c363
...
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@@ -2,7 +2,6 @@ Changelog
==========
<!--
Newest changes should be on top.
This document is user facing. Please word the changes in such a way
...
...
@@ -50,7 +49,7 @@ version 5.0.0-dev
+
Bam2fastx: Input bam and index are now arrays.
+
Lima: Remove globs from outputs.
+
Updated task gridss.wdl: add --jvmheap parameter.
+
A bwa-mem2 task was created with the same interface (including usePostalt)
+
A bwa-mem2 task was created with the same interface (including usePostalt)
as the bwa mem task.
+
bwa mem and bwa kit are now one task. The usePostalt boolean can be used to
switch the postalt script on and off.
...
...
@@ -91,7 +90,7 @@ version 4.0.0
file.
+
Added sambamba markdup and sambamba sort. NOTE: samtools sort is more
efficient and is recommended.
+
Correctly represent samtools inconsistent use of the threads flag.
+
Correctly represent samtools inconsistent use of the threads flag.
Sometimes it means 'threads' sometimes it means 'additional threads'.
BioWDL tasks now use only threads. The
`threads - 1`
conversion is
applied where necessary for samtools tools that use additional threads.
...
...
@@ -235,7 +234,7 @@ version 3.0.0
from going unnoticed.
+
Centrifuge: Fix -1/-U options for single end data.
+
Add bedtools.Complement, bedtools.Merge, and add a task to combine multiple
bed files called bedtools.MergeBedFiles. This task combines bedtools merge
bed files called bedtools.MergeBedFiles. This task combines bedtools merge
and sort.
+
Change
`g`
parameter on bedtools.Sort to
`genome`
.
+
Add
`ploidity`
and
`excludeIntervalList`
to gatk.HaplotypeCallerGvcf.
...
...
@@ -293,7 +292,7 @@ version 2.0.0
amount of containers needed.
+
Add biowdl-input-converter and remove SampleConfigToSampleReadgroupLists
which it replaces.
+
GATK.GenotypeGVCFs: Increased memoryMultiplier from 2.0 to 3.0
.
+
GATK.GenotypeGVCFs: Increased memoryMultiplier from 2.0 to 3.0.
+
Minimap2: Add -k option to minimap2 mapping.
+
Added bwakit task.
+
Minimap2: Add the option for --MD tag.
...
...
@@ -303,9 +302,7 @@ version 1.0.0
---------------------------
+
Common: Add "SampleConfigToSampleReadgroupLists" task.
+
MultiQC: the "interactive" input is now set to true by default.
+
Removed deprecated tasks:
+
bioconda.installPrefix
+
mergecounts.MergeCounts
+
Removed deprecated tasks: bioconda.installPrefix, mergecounts.MergeCounts
+
GATK.BaseRecalibrator: "knownIndelsSitesVCFs"
and "knownIndelsSitesVCFIndexes" are no longer optional, but
now have a default of "[]".
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README.md
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f111c363
# Tasks
This repository contains the WDL task definitions used in the various
This repository contains the WDL task definitions used in the various
[
Biowdl
](
https://github.com/biowdl
)
workflows and pipelines.
## Documentation
Documentation for this repository can be
found
[
here
](
https://biowdl.github.io/tasks/
)
.
Documentation for this repository can be
found
[
here
](
https://biowdl.github.io/tasks/
)
.
## About
These tasks are part of
[
Biowdl
](
https://github.com/biowdl
)
developed by the
SASC team at
[
Leiden University Medical Center
](
https://www.lumc.nl/
)
.
These tasks are part of
[
Biowdl
](
https://github.com/biowdl
)
developed by the
SASC team at
[
Leiden University Medical Center
](
https://www.lumc.nl/
)
.
## Contact
<p>
<!-- Obscure e-mail address for spammers -->
For any question related to
these t
asks, please use the
<a
href=
'
https://github.com/biowdl/tasks/issues
'
>
github issue tracker
</a>
For any question related to
T
asks, please use the
<a
href=
"
https://github.com/biowdl/tasks/issues
"
>
github issue tracker
</a>
or contact the SASC team directly at:
<a
href=
'
mailto:sasc@lumc.nl
'
>
<a
href=
"
mailto:sasc@lumc.nl
"
>
sasc@lumc.nl
</a>
.
</p>
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