update default parameters

Tom-Jenkins · Oct 28, 2024 · e739777 · e739777
1 parent b3d0596
commit e739777
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/env/variantcalling.yml b/env/variantcalling.yml
@@ -5,6 +5,6 @@ dependencies:
   - perl=5.32.1
   - bowtie2=2.5.3
   - samtools=1.19.2
-  - gatk4=4.5
+  - gatk4=4.4.0.0
   - bcftools=1.21
-  - freebayes=1.3.6
+  - freebayes=1.3.8
diff --git a/src/variantcalling.nf b/src/variantcalling.nf
@@ -9,7 +9,7 @@ params.outdir = "${PWD}"
 params.variantCaller = "both" // "bcftools" and "freebayes" or "both"
 params.bcftools_mpileup = "--min-MQ 40 --min-BQ 30"
 params.bcftools_call = "--ploidy 2 --multiallelic-caller --variants-only"
-params.freebayes_params = "-p 2 --min-mapping-quality 40 --min-base-quality 30 -g 200 --genotype-qualities"
+params.freebayes_params = "-p 2 --min-mapping-quality 40 --min-base-quality 30 --genotype-qualities"
 params.vcf = "variants"
 params.test = false
 params.cpus = 16