up changelog

Cristianetaniguti · Jan 5, 2024 · 4cbd7b7 · 4cbd7b7
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diff --git a/pipelines/EmpiricalMaps/EmpiricalMaps.changelog.md b/pipelines/EmpiricalMaps/EmpiricalMaps.changelog.md
@@ -1,3 +1,9 @@
+# 1.3.1
+
+* Make EmpiricalMaps for polyploids compatible with Reads2MapApp v0.0.2
+* Polyploid map quality diagnostic by resampling
+* Adapt regenotyping memory usage
+
 # 1.3.0
 
 * Add MAPpoly new functions framework_map and update_framework_map
@@ -7,7 +13,7 @@
 
 # 1.2.5
 
-* more flexibility to choose the probability to be used in the HMM: 
+* more flexibility to choose the probability to be used in the HMM:
 
 * new parameters:
 - global_errors: array with global errors to be tested

diff --git a/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md b/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md
@@ -1,3 +1,9 @@
+# 1.4.4
+
+* Make BarcodeFaker task work for input files that do not finish with .fasta or .fq
+* Adapt BarcodeFaker required memory and time
+* Adapt STACKs required memory
+
 # 1.4.3
 
 * Adapt tassel and stacks tasks also for polyploids
@@ -32,7 +38,7 @@
 # 1.2.0
 
 * Run freebayes parallelizing in nodes according to chromosomes and cores splitting in genomic regions
-* Adjust runtimes 
+* Adjust runtimes
 * Add polyploid dataset for tests
 
 # 1.1.0

diff --git a/tasks/gatk.wdl b/tasks/gatk.wdl
@@ -299,7 +299,7 @@ task VariantFiltration {
             -filter "QUAL < 30.0" --filter-name "QUAL30" \
             -filter "SOR > 3.0" --filter-name "SOR3" \
             -filter "FS > 60.0" --filter-name "FS60" \
-            -filter "MQ < 40.0" --filter-name "MQ50" \
+            -filter "MQ < 40.0" --filter-name "MQ40" \
             -filter "MQRankSum < -12.5" --filter-name "MQRankSum-12.5" \
             -filter "ReadPosRankSum < -8.0" --filter-name "ReadPosRankSum-8" \
             -O gatk_filters.vcf.gz