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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 ...@@ -2,7 +2,6 @@ Changelog
========== ==========
<!-- <!--
Newest changes should be on top. Newest changes should be on top.
This document is user facing. Please word the changes in such a way This document is user facing. Please word the changes in such a way
...@@ -50,7 +49,7 @@ version 5.0.0-dev ...@@ -50,7 +49,7 @@ version 5.0.0-dev
+ Bam2fastx: Input bam and index are now arrays. + Bam2fastx: Input bam and index are now arrays.
+ Lima: Remove globs from outputs. + Lima: Remove globs from outputs.
+ Updated task gridss.wdl: add --jvmheap parameter. + 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. as the bwa mem task.
+ bwa mem and bwa kit are now one task. The usePostalt boolean can be used to + bwa mem and bwa kit are now one task. The usePostalt boolean can be used to
switch the postalt script on and off. switch the postalt script on and off.
...@@ -91,7 +90,7 @@ version 4.0.0 ...@@ -91,7 +90,7 @@ version 4.0.0
file. file.
+ Added sambamba markdup and sambamba sort. NOTE: samtools sort is more + Added sambamba markdup and sambamba sort. NOTE: samtools sort is more
efficient and is recommended. 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'. Sometimes it means 'threads' sometimes it means 'additional threads'.
BioWDL tasks now use only threads. The `threads - 1` conversion is BioWDL tasks now use only threads. The `threads - 1` conversion is
applied where necessary for samtools tools that use additional threads. applied where necessary for samtools tools that use additional threads.
...@@ -235,7 +234,7 @@ version 3.0.0 ...@@ -235,7 +234,7 @@ version 3.0.0
from going unnoticed. from going unnoticed.
+ Centrifuge: Fix -1/-U options for single end data. + Centrifuge: Fix -1/-U options for single end data.
+ Add bedtools.Complement, bedtools.Merge, and add a task to combine multiple + 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. and sort.
+ Change `g` parameter on bedtools.Sort to `genome`. + Change `g` parameter on bedtools.Sort to `genome`.
+ Add `ploidity` and `excludeIntervalList` to gatk.HaplotypeCallerGvcf. + Add `ploidity` and `excludeIntervalList` to gatk.HaplotypeCallerGvcf.
...@@ -293,7 +292,7 @@ version 2.0.0 ...@@ -293,7 +292,7 @@ version 2.0.0
amount of containers needed. amount of containers needed.
+ Add biowdl-input-converter and remove SampleConfigToSampleReadgroupLists + Add biowdl-input-converter and remove SampleConfigToSampleReadgroupLists
which it replaces. 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. + Minimap2: Add -k option to minimap2 mapping.
+ Added bwakit task. + Added bwakit task.
+ Minimap2: Add the option for --MD tag. + Minimap2: Add the option for --MD tag.
...@@ -303,9 +302,7 @@ version 1.0.0 ...@@ -303,9 +302,7 @@ version 1.0.0
--------------------------- ---------------------------
+ Common: Add "SampleConfigToSampleReadgroupLists" task. + Common: Add "SampleConfigToSampleReadgroupLists" task.
+ MultiQC: the "interactive" input is now set to true by default. + MultiQC: the "interactive" input is now set to true by default.
+ Removed deprecated tasks: + Removed deprecated tasks: bioconda.installPrefix, mergecounts.MergeCounts
+ bioconda.installPrefix
+ mergecounts.MergeCounts
+ GATK.BaseRecalibrator: "knownIndelsSitesVCFs" + GATK.BaseRecalibrator: "knownIndelsSitesVCFs"
and "knownIndelsSitesVCFIndexes" are no longer optional, but and "knownIndelsSitesVCFIndexes" are no longer optional, but
now have a default of "[]". now have a default of "[]".
......
# Tasks # 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. [Biowdl](https://github.com/biowdl) workflows and pipelines.
## Documentation ## Documentation
Documentation for this repository can be found Documentation for this repository can be
[here](https://biowdl.github.io/tasks/). found [here](https://biowdl.github.io/tasks/).
## About ## About
These tasks are part of [Biowdl](https://github.com/biowdl) These tasks are part of [Biowdl](https://github.com/biowdl) developed by the
developed by the SASC team at [Leiden University Medical Center](https://www.lumc.nl/). SASC team at [Leiden University Medical Center](https://www.lumc.nl/).
## Contact ## Contact
<p> <p>
<!-- Obscure e-mail address for spammers --> <!-- Obscure e-mail address for spammers -->
For any question related to these tasks, please use the For any question related to Tasks, please use the
<a href='https://github.com/biowdl/tasks/issues'>github issue tracker</a> <a href="https://github.com/biowdl/tasks/issues">github issue tracker</a>
or contact the SASC team directly at: 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>. &#115;&#97;&#115;&#99;&#64;&#108;&#117;&#109;&#99;&#46;&#110;&#108;</a>.
</p> </p>
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