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Commit f111c363 authored by JasperBoom's avatar JasperBoom
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Update style.

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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 "[]".
......
# 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 tasks, please use the
<a href='https://github.com/biowdl/tasks/issues'>github issue tracker</a>
For any question related to Tasks, please use the
<a href="https://github.com/biowdl/tasks/issues">github issue tracker</a>
or contact the SASC team directly at:
<a href='&#109;&#97;&#105;&#108;&#116;&#111;&#58;&#115;&#97;&#115;&#99;&#64;&#108;&#117;&#109;&#99;&#46;&#110;&#108;'>
<a href="&#109;&#97;&#105;&#108;&#116;&#111;&#58;&#115;&#97;&#115;&#99;&#64;&#108;&#117;&#109;&#99;&#46;&#110;&#108;">
&#115;&#97;&#115;&#99;&#64;&#108;&#117;&#109;&#99;&#46;&#110;&#108;</a>.
</p>
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