Merge ba109be into c0dcde8

Clinical-Genomics · Jun 3, 2020 · 853b4fc · 853b4fc
2 parents c0dcde8 + ba109be
commit 853b4fc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,7 +17,9 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Add picardtools CollectRnaSeqMetrics to the RNA pipeline
 
 **Tools**
+- Arriba: 1.1.0 -> 1.2.0
 - bcftools: 1.9=ha228f0b_4 -> 1.10.2-hd2cd319_0 (DNA)
+- CADD: v1.5 -> v1.6
 - expansionhunter: 3.1.2 -> 3.2.2
 - fastqc: 0.11.8-0 -> 0.11.9
 - gatk: 4.1.3.0 -> 4.1.4.0
@@ -27,7 +29,6 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - samtools: 1.9=h8571acd_11 -> 1.10-h9402c20_2 (DNA)
 - SMNCopyNumberCaller: 4b2c1ad -> 1.0
 - VEP: 97 -> 99
-- CADD: v1.5 -> v1.6
 
 **References**
 - grch38_frequency_vcfanno_filter_config_-v1.2-.toml -> grch38_frequency_vcfanno_filter_config_-v1.3-.toml

diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
@@ -10,9 +10,9 @@ shell:
 singularity:
   arriba:
     executable:
-      arriba: /arriba_v1.1.0/arriba
-      draw_fusions.R: /arriba_v1.1.0/draw_fusions.R
-    uri: docker://uhrigs/arriba:1.1.0
+      arriba: /arriba_v1.2.0/arriba
+      draw_fusions.R: /arriba_v1.2.0/draw_fusions.R
+    uri: docker://uhrigs/arriba:1.2.0
   blobfish:
     executable:
       BlobFish.py:

diff --git a/templates/mip_rd_rna_config.yaml b/templates/mip_rd_rna_config.yaml
@@ -26,9 +26,9 @@ transcript_annotation: grch37_gencode_annotation_reformated_-v31-.gtf
 ### Analysis
 ## Programs
 ## Parameters
-arriba_blacklist_path: /arriba_v1.1.0/database/blacklist_hg19_hs37d5_GRCh37_2018-11-04.tsv.gz
-arriba_cytoband_path: /arriba_v1.1.0/database/cytobands_hg19_hs37d5_GRCh37_2018-02-23.tsv
-arriba_proteindomain_path: /arriba_v1.1.0/database/protein_domains_hg19_hs37d5_GRCh37_2018-03-06.gff3
+arriba_blacklist_path: /arriba_v1.2.0/database/blacklist_hg19_hs37d5_GRCh37_2018-11-04.tsv.gz
+arriba_cytoband_path: /arriba_v1.2.0/database/cytobands_hg19_hs37d5_GRCh37_2018-02-23.tsv
+arriba_proteindomain_path: /arriba_v1.2.0/database/protein_domains_hg19_hs37d5_GRCh37_2019-07-05.gff3
 picardtools_path: /usr/picard
 qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml
 vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-99/cache/