updated deepvariant, deeptrio, and star-fusion

CHANGELOG.md

@@ -10,12 +10,15 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ### Tools
 
-HmtNote: 0.7.2
-htslib: 1.10.2 -> 1.13
 cyrius v1.1 -> v1.1.1
+deepvariant 1.1.0-gpu -> 1.2.0-gpu
+deeptrio 1.1.0-gpu -> 1.2.0-gpu
 gatk 4.2.0.0 -> 4.2.2.0
 glnexus v1.3.1 -> v1.4.1
+HmtNote: 0.7.2
+htslib: 1.10.2 -> 1.13
 multiqc 1.10.1 -> v1.11
+star-fusion 1.10.0 -> 1.10.1
 vep release_103.1 -> release_104.3
 
 ### References

documentation/Setup.md

@@ -48,7 +48,8 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [Cyrius] (version: v1.1.1)
 - [Expansionhunter] (version 4.0.2)
 - [FastQC] (version: 0.11.9)
-- [Deepvariant] (version: 1.1.0)
+- [Deeptrio] (version: 1.2.0)
+- [Deepvariant] (version: 1.2.0)
 - [Delly] (version 0.8.7)
 - [GATK] (version: 3.8.1 and 4.2.2.0)
 - [GENMOD] (version: 3.7.3)
@@ -70,7 +71,7 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [Sambamba] (version: 0.6.8)
 - [Samtools] (version: 1.11)
 - [SMNCopyNumberCaller] (version: v1.1.1)
-- [STAR-Fusion] (version: 1.10.0)
+- [STAR-Fusion] (version: 1.10.1)
 - [STAR] (version: 2.7.8a)
 - [Stranger] (version: 0.8.0)
 - [StringTie] (version: 2.1.3b)

templates/mip_install_config.yaml

@@ -60,12 +60,12 @@ container:
       call_variants: /opt/deepvariant/bin/call_variants
       postprocess_variants: /opt/deepvariant/bin/postprocess_variants
     gpu_support: 1
-    uri: docker.io/google/deepvariant:1.1.0-gpu
+    uri: docker.io/google/deepvariant:1.2.0-gpu
   deeptrio:
     executable:
       run_deeptrio: /opt/deepvariant/bin/deeptrio/run_deeptrio
     gpu_support: 1
-    uri: docker.io/google/deepvariant:deeptrio-1.1.0-gpu
+    uri: docker.io/google/deepvariant:deeptrio-1.2.0-gpu
   delly:
     executable:
       delly:
@@ -197,7 +197,7 @@ container:
       remove_long_intron_readthru_transcripts.pl: /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/remove_long_intron_readthru_transcripts.pl
       restrict_genome_to_chr_entries.pl: /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/restrict_genome_to_chr_entries.pl
       STAR-Fusion: /usr/local/src/STAR-Fusion/STAR-Fusion
-    uri: docker.io/trinityctat/starfusion:1.10.0
+    uri: docker.io/trinityctat/starfusion:1.10.1
   stranger:
     executable:
       stranger: