From f111c363b74ec64ee7ba06db7a7ad2b3f3ada05a Mon Sep 17 00:00:00 2001 From: JasperBoom <jboom@infernum.nl> Date: Tue, 10 Nov 2020 17:00:31 +0100 Subject: [PATCH] Update style. --- CHANGELOG.md | 13 +++++-------- README.md | 16 ++++++++-------- 2 files changed, 13 insertions(+), 16 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 836af4a..0b668ab 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 "[]". diff --git a/README.md b/README.md index 9d682de..2c80e31 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,21 @@ # 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='mailto:sasc@lumc.nl'> +<a href="mailto:sasc@lumc.nl"> sasc@lumc.nl</a>. </p> -- GitLab