From 29c5d4da36dafed4e878466b177851557a2fc375 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen Date: Wed, 11 Oct 2023 11:34:28 +0200 Subject: [PATCH 1/2] Updating link to entieonDNAscopeModel file --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 56cab933a6..ca6e2ed00a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -70,7 +70,7 @@ params { joint_mutect2 = false // if true, enables patient-wise multi-sample somatic variant calling only_paired_variant_calling = false // if true, skips germline variant calling for normal-paired sample sentieon_dnascope_emit_mode = "variant" // default value for Sentieon dnascope - sentieon_dnascope_model = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model" + sentieon_dnascope_model = "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model" sentieon_dnascope_pcr_indel_model = "CONSERVATIVE" sentieon_haplotyper_emit_mode = "variant" // default value for Sentieon haplotyper wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers From c325cd453d091238ac4745112bb6d8a20c031d14 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen Date: Wed, 11 Oct 2023 11:41:46 +0200 Subject: [PATCH 2/2] Updating changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 60d93f7426..7e9f3a0458 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,11 +9,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline. +- [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline - [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev ### Changed +- [#1280](https://github.com/nf-core/sarek/pull/1280) - Replacing link to `SentieonDNAscopeModel1.1.model` in Sentieon's S3 with link to same file in igenomes' S3 + ### Fixed ### Dependencies