From 28178b18890e61ce0a1094d188d3a31d18b03b6f Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 23 May 2023 16:39:10 +0200 Subject: [PATCH] Use latest zenodo data with fixed CIVic.bed Previous version of the bed file contained two lines with START > STOP, which caused recent version of tabix to refuse indexing the file. --- .../tutorials/somatic-variants/tutorial.md | 8 ++++---- .../workflows/somatic_variants_tutorial_workflow-test.yml | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/topics/variant-analysis/tutorials/somatic-variants/tutorial.md b/topics/variant-analysis/tutorials/somatic-variants/tutorial.md index f6986467a7ebc..d9388cb310fef 100644 --- a/topics/variant-analysis/tutorials/somatic-variants/tutorial.md +++ b/topics/variant-analysis/tutorials/somatic-variants/tutorial.md @@ -685,12 +685,12 @@ license. > Data upload > > 1. Import the following **variant annotation files** from -> [Zenodo](https://zenodo.org/record/2581873): +> [Zenodo](https://zenodo.org/record/7962928): > > ``` -> https://zenodo.org/record/2581873/files/hotspots.bed -> https://zenodo.org/record/2581873/files/cgi_variant_positions.bed -> https://zenodo.org/record/2581873/files/01-Feb-2019-CIVic.bed +> https://zenodo.org/record/7962928/files/hotspots.bed +> https://zenodo.org/record/7962928/files/cgi_variant_positions.bed +> https://zenodo.org/record/7962928/files/01-Feb-2019-CIVic.bed > https://zenodo.org/record/2582555/files/dbsnp.b147.chr5_12_17.vcf.gz > ``` > diff --git a/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow-test.yml b/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow-test.yml index 26a235a1b24b1..d60385d1915c4 100644 --- a/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow-test.yml +++ b/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow-test.yml @@ -23,15 +23,15 @@ filetype: fasta hotspots.bed: class: File - location: https://zenodo.org/record/2581873/files/hotspots.bed + location: https://zenodo.org/record/7962928/files/hotspots.bed filetype: bed cgi_variant_positions.bed: class: File - location: https://zenodo.org/record/2581873/files/cgi_variant_positions.bed + location: https://zenodo.org/record/7962928/files/cgi_variant_positions.bed filetype: bed 01-Feb-2019-CIVic.bed: class: File - location: https://zenodo.org/record/2581873/files/01-Feb-2019-CIVic.bed + location: https://zenodo.org/record/7962928/files/01-Feb-2019-CIVic.bed filetype: bed Uniprot_Cancer_Genes.13Feb2019.txt: class: File