From ae67e0877c6d4f490284081f4a75a1999ff272b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Fri, 26 Jul 2019 15:17:31 +0200
Subject: [PATCH] update -M and -A flags to be inputs and attributes
unnecessarily marked as optional update changelog
---
CHANGELOG.md | 1 +
vardict.wdl | 14 ++++++++------
2 files changed, 9 insertions(+), 6 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bcdcc6f..ddc6085 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
version 1.0.0-dev
---------------------------
++ VarDict: Add user definable flags (-M, -A, -Q, -d, -v, -f) to the paired VCF filtering script.
+ Cutadapt: If the output is a gzipped file, compress with level 1 (instead of default 6).
+ Cutadapt: Fix issues with read2output when using single-end reads.
+ Add feature type, idattr and additional attributes to htseq-count.
diff --git a/vardict.wdl b/vardict.wdl
index 069d866..69a5441 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -20,10 +20,12 @@ task VarDict {
Int endColumn = 3
Int geneColumn = 4
- Float? mappingQuality = 20
- Int? minimumTotalDepth = 8
- Int? minimumVariantDepth = 4
- Float? minimumAlleleFrequency = 0.02
+ Boolean outputCandidateSomaticOnly = true
+ Boolean outputAllVariantsAtSamePosition = true
+ Float mappingQuality = 20
+ Int minimumTotalDepth = 8
+ Int minimumVariantDepth = 4
+ Float minimumAlleleFrequency = 0.02
Int threads = 1
Int memory = 16
@@ -50,8 +52,8 @@ task VarDict {
~{true="var2vcf_paired.pl" false="var2vcf_valid.pl" defined(normalBam)} \
-N "~{tumorSampleName}~{"|" + normalSampleName}" \
~{true="" false="-E" defined(normalBam)} \
- -M \
- -A \
+ ~{true="-M" false="" outputCandidateSomaticOnly} \
+ ~{true="-A" false="" outputAllVariantsAtSamePosition} \
-Q ~{mappingQuality} \
-d ~{minimumTotalDepth} \
-v ~{minimumVariantDepth} \
--
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