Merge pull request #2043 from Clinical-Genomics/release/12.0.0

Release/12.0.0

Author: jemten

CHANGELOG.md

@@ -3,21 +3,55 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [12.0.0]
+
+- Set overlap requirement for merging two SVs to 0.8, down from the 0.95 default
+- Set overlap requirement for SV annotation to 0.6, up from 0.5
+- Update Tiddit to improve SV positioning
+- Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)
+- New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
+- Remove the RSeQC read duplication analysis as it often fails.
+- Increased run time allocation for gatk_asereadcounter.
+- Increased the default required length for a trimmed rna read to be retained from 20 bp to 40 bp. Configurable via CLI or config.
+- Fixed a bug where gnomad SV version 2.0 instead of version 2.1 was used to annotate SVs
+- One-pass instead of two-pass mapping with STAR-Fusion, as recommended for STAR-Fusion 1.12
+- Bump max run time for retroseq to 15 hours.
+
+### Tools
+
+- Arriba 2.3.0 -> 2.4.0
+- DeepVariant 1.4.0 -> 1.5.0
+- FastQC: 0.11.9 -> 0.12.1
+- GATK: 4.2.6.1 -> 4.4.0.0
+- Gffcompare 0.11.2 -> 0.12.6
+- Htslib 1.15.1 -> 1.16
+- MegaFusion 66a3a80 -> d3feacf
+- Picard 2.27.2 -> 2.27.5
+- STAR-Fusion 1.11.0 -> 1.12.0
+- SVDB: 2.7.0 -> 2.8.2
+- Tiddit 3.3.2 -> 3.6.0
+
+### Databases
+
+clinvar: 20220829 -> 20230508
+loqusdb snapshot: 20230208 -> 20230512
+hmtvar: oct2022
+
 ## [11.2.2]
 
 - New patch of gens pre processing container.
 
 ### Tools
 
-gens_preproc 1.0.8 -> 1.0.11
+- gens_preproc 1.0.8 -> 1.0.11
 
 ## [11.2.1]
 
 - Patching of gens pre processing container to solve an issue with incomplete bed files.
 
 ### Tools
 
-gens_preproc 1.0.2 -> 1.0.8
+- gens_preproc 1.0.2 -> 1.0.8
 
 ## [11.2.0]
 
@@ -88,7 +122,7 @@ gens_preproc 1.0.2 -> 1.0.8
 - dbnsfp: 4.1a -> 4.3a (grch38 only)
 - gnomad: r3.1.1 -> r3.1.2 (grch38 only)
 - giab: 3.3.2 -> 4.2.1
-- loqusdb dump: 20210921 -> 20220905
+- loqusdb dump: 20210921 -> c
 - nist: v3.3.2 -> v4.2.1
 - vcf2cytosure blacklist: 200520
 

containers/fastqc/Dockerfile

@@ -5,15 +5,13 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="2"
+LABEL version="3"
 LABEL software="fastqc"
-LABEL software.version="0.11.9"
+LABEL software.version="0.12.1"
 LABEL extra.binaries="fastqc"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install fastqc=0.11.9=0
-
-## Clean up after conda
-RUN /opt/conda/bin/conda clean -tipsy
+RUN conda install fastqc=0.12.1 && \
+    /opt/conda/bin/conda clean -ya
 
 WORKDIR /data/

containers/gffcompare/Dockerfile

@@ -5,15 +5,15 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base-image="clinicalgenomics/mip_base:2.1"
-LABEL version="1"
+LABEL version="2"
 LABEL software="HmtNote"
 LABEL software.version="0.7.2"
-LABEL extra.binaries="HmtNote"
+LABEL extra.binaries="HmtNote, hmtvar_oct2022"
 LABEL maintainer="Clinical-Genomics/MIP"
 
 ## Conda env installation + clean up
 RUN conda install pip python=3.7 && \
-    /opt/conda/bin/conda clean -tipsy
+    /opt/conda/bin/conda clean -ya
 
 # Install HmtNote
 RUN pip install --no-cache-dir hmtnote==0.7.2 && \

containers/hmtnote/Dockerfile

@@ -5,13 +5,13 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base-image="clinicalgenomics/mip_base:2.1"
-LABEL version="7"
+LABEL version="8"
 LABEL software="htslib"
-LABEL software.version="1.15.1"
+LABEL software.version="1.16"
 LABEL extra.binaries="bcftools, bgzip, samtools, tabix"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install bcftools=1.15.1 htslib=1.15.1 samtools=1.15.1 && \
+RUN conda install bcftools=1.16 htslib=1.16 samtools=1.16.1 && \
     /opt/conda/bin/conda clean -ya
 
 WORKDIR /data/

containers/htslib/Dockerfile

@@ -7,7 +7,7 @@ FROM clinicalgenomics/mip_base:2.1
 LABEL base_image="clinicalgenomics/mip_base:2.1"
 LABEL version="4"
 LABEL software="MegaFusion"
-LABEL software.version="66a3a80"
+LABEL software.version="d3feacf"
 LABEL extra.binaries="MegaFusion.py"
 LABEL maintainer="Clinical-Genomics/MIP"
 
@@ -25,5 +25,5 @@ RUN git clone https://github.com/J35P312/MegaFusion.git /opt/conda/share/MegaFus
 WORKDIR /opt/conda/share/MegaFusion
 
 ## Make sure we're on the right commit
-RUN git reset --hard 66a3a80
+RUN git reset --hard d3feacf
 

containers/megafusion/Dockerfile

@@ -377,7 +377,7 @@ recipe_time:
     prepareforvariantannotationblock: 5
     qccollect_ar: 1
     rankvariant: 10
-    retroseq: 5
+    retroseq: 15
     rhocall_ar: 5
     rhocall_viz: 1
     rtg_vcfeval: 1
@@ -959,6 +959,12 @@ sv_svdb_merge_prioritize:
   data_type: SCALAR
   default: tiddit,cnvnator,manta
   type: recipe_argument
+sv_svdb_merge_overlap:
+  associated_recipe:
+    - sv_combinevariantcallsets
+  data_type: SCALAR
+  default: 0.8
+  type: recipe_argument
 sv_decompose:
   associated_recipe:
     - sv_combinevariantcallsets
@@ -1015,7 +1021,7 @@ sv_svdb_query_overlap:
   associated_recipe:
     - sv_annotate
   data_type: SCALAR
-  default: 0.5
+  default: 0.6
   type: recipe_argument
 sv_vcfanno_config:
   associated_recipe:

definitions/rd_dna_parameters.yaml

@@ -146,7 +146,7 @@ recipe_time:
     dna_vcf_reformat: 1
     fastqc_ar: 1
     fusion_report: 8
-    gatk_asereadcounter: 3
+    gatk_asereadcounter: 8
     gatk_baserecalibration: 5
     gatk_haplotypecaller: 12
     gatk_splitncigarreads: 16
@@ -191,10 +191,10 @@ recipe_memory:
     merge_fusion_reports: 8
     multiqc_ar: 10
     picardtools_collectrnaseqmetrics: 10
-    picardtools_mergesamfiles: 5
+    picardtools_mergesamfiles: 8
     preseq_ar: 8
     rseqc: 40
-    salmon_quant: 2
+    salmon_quant: 4
     star_aln: 5
     star_fusion: 25
     stringtie_ar: 2
@@ -301,6 +301,13 @@ trim_galore_ar:
   program_executables:
     - trim_galore
   type: recipe
+trim_min_length:
+  associated_recipe:
+    - trim_galore_ar
+  data_type: SCALAR
+  default: 40
+  mandatory: no
+  type: recipe_argument
 ## Salmon
 salmon_quant:
   analysis_mode: sample

definitions/rd_rna_parameters.yaml

@@ -76,9 +76,9 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [STAR] (version: 2.7.8a)
 - [Stranger] (version: 0.8.0)
 - [StringTie] (version: 2.1.3b)
-- [Svdb] (version: 2.4.0)
+- [Svdb] (version: 2.8.2)
 - [Telomerecat] (version: 3.4.0)
-- [Tiddit] (version: 2.12.1)
+- [Tiddit] (version: 3.6.0)
 - [Upd] (version: 0.1.1)
 - [Varg] (version: 1.2.0)
 - [Vcf2cytosure] (version: 0.5.1)

documentation/Setup.md

@@ -827,6 +827,14 @@ q{Default: grch37_dbsnp_-138-.vcf, grch37_1000g_indels_-phase1-.vcf, grch37_mill
         )
     );
 
+    option(
+        q{sv_svdb_merge_overlap} => (
+            documentation => q{Required overlap to merge two structural variants},
+            is            => q{rw},
+            isa           => Num,
+        )
+    );
+
     option(
         q{sv_svdb_merge_prioritize} => (
             documentation => q{Prioritization order of structural variant callers},
@@ -897,7 +905,7 @@ q{Default: grch37_dbsnp_-138-.vcf, grch37_1000g_indels_-phase1-.vcf, grch37_mill
         q{sv_svdb_query_overlap} => (
             documentation => q{Database file(s) for annotation},
             is            => q{rw},
-            isa           => Str,
+            isa           => Num,
         )
     );