From 99215fdd9834f39569e5672b9daf5b010a777abc Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 26 Jan 2022 12:56:23 +0100
Subject: [PATCH] update scripts and changelog
---
CHANGELOG.md | 37 +++++++++++++++++++++++++++++++++++++
bcftools.wdl | 4 ++--
scripts | 2 +-
3 files changed, 40 insertions(+), 3 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 126f1ed..6c0db94 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,43 @@ that users understand how the changes affect the new version.
-->
version 5.1.0-dev
---------------------------
++ Added a task for SnpEff.
++ Adjusted runtime settings for sambamba Markdup.
++ Added a task for sambamba Flagstat.
++ Added a task for Picard CollectWgsMetrics.
++ Added a task for Peach.
++ Added tasks for HMFtools:
+ + Amber
+ + Cobalt
+ + Cuppa
+ + CuppaChart
+ + GripssApplicationKt
+ + GripssHardFilterApplicationKt
+ + HealthChecker
+ + Linx
+ + Protect
+ + Purple
+ + Sage
+ + VirusInterpreter
++ Added a task for VirusBreakend.
++ Added a task for GridssAnnotateVcfRepeatmasker.
++ Bumped GRIDSS version to 2.12.2.
++ Adjusted GRIDSS runtime settings.
++ Added optional inputs to GRIDSS:
+ + blacklistBed
+ + gridssProperties
++ Added a task for GRIDSS AnnotateInsertedSequence.
++ Added a task for ExtractSigPredictHRD.
++ Added a task for DeconstructSigs.
++ Added option useSoftclippingForSupplementary (default false) to
+ BWA mem.
++ Adjusted BWA mem runtime settings.
++ Added a task for bedtools coverage.
++ Added a task for bcftools filter.
++ Adjusted runtime settings for bcftools annotate.
++ Added optional inputs to bcftools annotate:
+ + inputFileIndex
+ + annsFileIndex
+ Update parameter_meta for macs2
+ Add sample position in array task.
diff --git a/bcftools.wdl b/bcftools.wdl
index 13ce36b..88d97cd 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -44,8 +44,8 @@ task Annotate {
String? regions
File? regionsFile
File? renameChrs
- File? samplesFile
-
+ File? samplesFile
+
Int threads = 0
String memory = "4G"
Int timeMinutes = 60 + ceil(size(inputFile, "G"))
diff --git a/scripts b/scripts
index c31670d..84690a3 160000
--- a/scripts
+++ b/scripts
@@ -1 +1 @@
-Subproject commit c31670d3a9222a2feafc649cbc118c95afbc7189
+Subproject commit 84690a30eb0dde2bfdfaff9abf097b6f4c49dfd8
--
GitLab