From e7397773f24f0ef3f9e2a2106e2d89e39f72a485 Mon Sep 17 00:00:00 2001 From: Jenkins Date: Mon, 28 Oct 2024 10:50:43 +0000 Subject: [PATCH] update default parameters --- env/variantcalling.yml | 4 ++-- src/variantcalling.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/env/variantcalling.yml b/env/variantcalling.yml index 1469262..8282cb0 100644 --- 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 \ No newline at end of file + - freebayes=1.3.8 \ No newline at end of file diff --git a/src/variantcalling.nf b/src/variantcalling.nf index 253a107..d2daec9 100644 --- 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