Merge pull request #1967 from Clinical-Genomics/release/11.0.0

Release/11.0.0

CHANGELOG.md

@@ -3,6 +3,34 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [11.0.0]
+
+- HmtNote: annotate mitochondrial variants in VCF file
+- Updating to latest and greatest versions
+- Mitochondrial deletion analysis
+- GATK Haplotypecaller has been turned off in favour of Deepvariant
+- Introduces possibility to store singularity images locally as a .sif file
+- Increased allele frequency cut off for when a variant is filtered out to 0.7
+- Turned off Star_caller and Telomerecat by default
+
+### Tools
+
+cyrius v1.1 -> v1.1.1
+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
+
+- gnomad: r3.0 -> r3.1.1
+- [NEW] gnomad mt: r3.1
+- clinvar: 20210415 -> 20211010
+
 ## [10.2.5]
 
 - Allow slurm quality of service flag to be set to 'express'

README.md

@@ -13,6 +13,13 @@ MIP enables identification of potential disease causing variants from sequencing
 
 ## Citing MIP
 
+```
+Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients
+Stranneheim H, Lagerstedt-Robinson K, Magnusson M, Kvarnung M, Nilsson D, Lesko N, Engvall M, Anderlid BM, Arnell H, Johansson CB, Barbaro M, Björck E, Bruhn H, Eisfeldt J, Freyer C, Grigelioniene G, Gustavsson P, Hammarsjö A, Hellström-Pigg M, Iwarsson E, Jemt A, Laaksonen M, Enoksson SL, Malmgren H, Naess K, Nordenskjöld M, Oscarson M, Pettersson M, Rasi C, Rosenbaum A, Sahlin E, Sardh E, Stödberg T, Tesi B, Tham E, Thonberg H, Töhönen V, von Döbeln U, Vassiliou D, Vonlanthen S, Wikström AC, Wincent J, Winqvist O, Wredenberg A, Ygberg S, Zetterström RH, Marits P, Soller MJ, Nordgren A, Wirta V, Lindstrand A, Wedell A.
+Genome Med. 2021 Mar 17;13(1):40. doi: 10.1186/s13073-021-00855-5.
+PMID: 33726816; PMCID: PMC7968334.
+```
+
 ```
 Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism
 Stranneheim H, Engvall M, Naess K, Lesko N, Larsson P, Dahlberg M, Andeer R, Wredenberg A, Freyer C, Barbaro M, Bruhn H, Emahazion T, Magnusson M, Wibom R, Zetterström RH, Wirta V, von Döbeln U, Wedell A.
@@ -22,6 +29,9 @@ PMID:25495354
 
 ## Overview
 
+**MIP is being rewritten in NextFlow as a part of the [nf-core](https://nf-co.re/) project. This repo will mainly receive bugfixes as we are focusing our resources on the new pipeline.**  
+**You can follow the progress here :point_right: [raredisease](https://github.com/nf-core/raredisease).**
+
 MIP performs whole genome or target region analysis of sequenced single-end and/or paired-end reads from the Illumina platform in fastq\(.gz\) format to generate annotated ranked potential disease causing variants.
 
 MIP performs QC, alignment, coverage analysis, variant discovery and annotation, sample checks as well as ranking the found variants according to disease potential with a minimum of manual intervention. MIP is compatible with [Scout](https://github.com/Clinical-Genomics/scout) for visualization of identified variants.
@@ -223,6 +233,6 @@ MIP will place any generated data files in the output data directory specified b
 [Miniconda]: http://conda.pydata.org/miniconda.html
 [Pedigree file]: https://github.com/Clinical-Genomics/MIP/tree/master/templates/643594-miptest_pedigree.yaml
 [Perl]:https://www.perl.org/
-[Rank model file]: https://github.com/Clinical-Genomics/MIP/blob/master/templates/rank_model_-v1.31-.ini
+[Rank model file]: https://github.com/Clinical-Genomics/MIP/blob/master/templates/rank_model_-v1.33-.ini
 [SV rank model file]: https://github.com/Clinical-Genomics/MIP/blob/master/templates/svrank_model_-v1.8-.ini
 [Qc regexp file]: https://github.com/Clinical-Genomics/MIP/blob/master/templates/qc_regexp_-v1.26-.yaml

containers/bootstrapann/Dockerfile

@@ -1,33 +1,30 @@
 ################## BASE IMAGE ######################
 
-FROM continuumio/miniconda3:4.7.12
+FROM python:2.7-slim
 
 ################## METADATA ######################
 
-LABEL base_image="continuumio/miniconda3:4.7.12"
+LABEL base_image="python:2.7-slim"
 LABEL version="2"
 LABEL software="BootstrapAnn"
-LABEL software.version="df02f35"
+LABEL software.version="e557dd3"
 LABEL extra.binaries="BootstrapAnn.py"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN apt-get --allow-releaseinfo-change update --fix-missing && \
-    apt-get install -y --no-install-recommends procps && \
-    apt-get clean && \
+RUN apt-get update && apt-get install -y git
+RUN apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-RUN conda install pip python=2.7 numpy scipy && \
-    /opt/conda/bin/conda clean -ya
+RUN pip install numpy scipy
 
 ## Clone git repository
-RUN git clone https://github.com/J35P312/BootstrapAnn.git /opt/conda/share/BootstrapAnn
+RUN git clone https://github.com/J35P312/BootstrapAnn.git /usr/local/BootstrapAnn
 
-WORKDIR /opt/conda/share/BootstrapAnn
+RUN cd /usr/local/BootstrapAnn && git checkout e557dd3
 
-RUN git checkout df02f35
+RUN cd /usr/local/BootstrapAnn && \
+    chmod a+x BootstrapAnn.py
 
-RUN chmod a+x BootstrapAnn.py
-
-RUN ln --symbolic --force /opt/conda/share/BootstrapAnn/BootstrapAnn.py /opt/conda/bin/BootstrapAnn.py
+RUN ln --symbolic --force /usr/local/BootstrapAnn/BootstrapAnn.py /usr/local/bin/BootstrapAnn.py
 
 WORKDIR /data/

containers/chromograph/Dockerfile

@@ -17,20 +17,14 @@ RUN apt-get update --fix-missing && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-RUN conda install pip python=3.9 matplotlib
+RUN conda install pip python=3.9 matplotlib && \
+    /opt/conda/bin/conda clean -ya
 
-## Clean up after conda
-RUN /opt/conda/bin/conda clean -ya
+WORKDIR /opt/conda/share
 
-## Download release
-RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/refs/tags/v1.1.4.zip -O /opt/conda/share/chromograph-1.1.4.zip
-
-## Extract
-RUN unzip -o /opt/conda/share/chromograph-1.1.4.zip -d /opt/conda/share/ && \
-    rm /opt/conda/share/chromograph-1.1.4.zip
-
-## Move to chromograph directory
-RUN cd /opt/conda/share/chromograph-1.1.4 && \
+RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/refs/tags/v1.1.4.zip && \
+    unzip v1.1.4.zip && \
+    cd chromograph-1.1.4 && \
     python -m pip install --no-cache-dir .
 
 WORKDIR /data/

containers/cyrius/Dockerfile

@@ -4,28 +4,28 @@ FROM clinicalgenomics/mip_base:2.1
 
 ################## METADATA ######################
 
-LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="2"
+LABEL base-image="clinicalgenomics/mip_base:2.1"
+LABEL version="3"
 LABEL software="Cyrius"
-LABEL software.version="v1.1"
+LABEL software.version="v1.1.1"
 LABEL extra.binaries="star_caller.py"
 LABEL maintainer="Clinical-Genomics/MIP"
 
 WORKDIR /opt/conda/share
 
 ## Pysam errors when pip installing
-RUN conda install pysam=0.16.0 && \
+RUN conda install pysam=0.16.0.1 && \
     conda clean -ya
 
 ## Download and extract
-RUN wget --no-verbose --no-check-certificate https://github.com/Illumina/Cyrius/archive/v1.1.zip && \
-    unzip v1.1.zip && \
-    rm v1.1.zip
+RUN wget --no-verbose --no-check-certificate https://github.com/Illumina/Cyrius/archive/v1.1.1.zip && \
+    unzip v1.1.1.zip && \
+    rm v1.1.1.zip
 
 ## Move to directory and install requirements
-RUN cd Cyrius-1.1 && \
-   python -m pip install --no-cache-dir -r requirements.txt
+RUN cd Cyrius-1.1.1 && \
+    python -m pip install --no-cache-dir -r requirements.txt
 
-RUN chmod a+x /opt/conda/share/Cyrius-1.1/star_caller.py
+RUN chmod a+x /opt/conda/share/Cyrius-1.1.1/star_caller.py
 
-ENV PATH ${PATH}:/opt/conda/share/Cyrius-1.1
+ENV PATH ${PATH}:/opt/conda/share/Cyrius-1.1.1

containers/glnexus/Dockerfile

@@ -0,0 +1,26 @@
+################## BASE IMAGE ######################
+
+FROM clinicalgenomics/mip_base:2.1
+
+################## METADATA ######################
+
+LABEL base-image="clinicalgenomics/mip_base:2.1"
+LABEL version="1"
+LABEL software="glnexus"
+LABEL software.version="1.4.1"
+LABEL extra.binaries="glnexus"
+LABEL maintainer="Clinical-Genomics/MIP"
+
+WORKDIR /app
+
+ENV PATH="/app:${PATH}"
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+            libc6 \
+            ca-certificates && \
+    apt-get clean && \
+    apt-get purge && \
+    rm -rf /var/lib/apt/lists/* && \
+    wget --no-verbose https://github.com/dnanexus-rnd/GLnexus/releases/download/v1.4.1/glnexus_cli && \
+    chmod 755 /app/glnexus_cli

containers/hmtnote/Dockerfile

@@ -0,0 +1,22 @@
+################## BASE IMAGE ######################
+
+FROM clinicalgenomics/mip_base:2.1
+
+################## METADATA ######################
+
+LABEL base-image="clinicalgenomics/mip_base:2.1"
+LABEL version="1"
+LABEL software="HmtNote"
+LABEL software.version="0.7.2"
+LABEL extra.binaries="HmtNote"
+LABEL maintainer="Clinical-Genomics/MIP"
+
+## Conda env installation + clean up
+RUN conda install pip python=3.7 && \
+    /opt/conda/bin/conda clean -tipsy
+
+# Install HmtNote
+RUN pip install --no-cache-dir hmtnote==0.7.2 && \
+    hmtnote dump
+
+WORKDIR /data/

containers/htslib/Dockerfile

@@ -1,17 +1,17 @@
 ################## BASE IMAGE ######################
 
-FROM clinicalgenomics/mip_base:2.0
+FROM clinicalgenomics/mip_base:2.1
 
 ################## METADATA ######################
 
-LABEL base_image="clinicalgenomics/mip_base:2.0"
-LABEL version="5"
+LABEL base-image="clinicalgenomics/mip_base:2.1"
+LABEL version="6"
 LABEL software="htslib"
-LABEL software.version="1.10.2"
+LABEL software.version="1.13"
 LABEL extra.binaries="bcftools, bgzip, samtools, tabix"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install bcftools=1.10.2=hd2cd319_0 htslib=1.10.2=h78d89cc_0 samtools=1.10=h9402c20_2
+RUN conda install bcftools=1.13=h3a49de5_0 htslib=1.13=h9093b5e_0 samtools=1.13=h8c37831_0
 
 ## Clean up after conda
 RUN /opt/conda/bin/conda clean -ya

definitions/analyse_parameters.yaml

@@ -84,7 +84,7 @@ case_id:
     - mip
   data_type: SCALAR
   type: mip
-install_config_file:
+container_config_file:
   associated_recipe:
     - mip
   data_type: SCALAR
@@ -168,6 +168,12 @@ project_id:
     - mip
   data_type: SCALAR
   type: mip
+recipe_bind_path:
+  associated_recipe:
+    - mip
+  data_type: HASH
+  mandatory: no
+  type: mip
 reference_dir:
   associated_recipe:
     - mip
@@ -192,7 +198,19 @@ sample_info_file:
   data_type: SCALAR
   type: path
   update_path: absolute_path
-recipe_bind_path:
+set_recipe_core_number:
+  associated_recipe:
+    - mip
+  data_type: HASH
+  mandatory: no
+  type: mip
+set_recipe_memory:
+  associated_recipe:
+    - mip
+  data_type: HASH
+  mandatory: no
+  type: mip
+set_recipe_time:
   associated_recipe:
     - mip
   data_type: HASH

definitions/download_parameters.yaml

@@ -124,7 +124,7 @@ custom_default_parameters:
     - mip
   data_type: ARRAY
   default:
-    - install_config_file
+    - container_config_file
     - reference_dir
     - temp_directory
   type: mip
@@ -240,6 +240,24 @@ gnomad:
     - tabix
     - vcfanno
   type: recipe
+gnomad_chrsplit:
+  analysis_mode: case
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  default: 1
+  program_executables:
+    - bcftools
+    - bgzip
+    - tabix
+  type: recipe
+gnomad_mt:
+  analysis_mode: case
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  default: 1
+  type: recipe
 gnomad_pli_per_gene:
   analysis_mode: case
   associated_recipe:
@@ -263,7 +281,7 @@ human_reference:
   program_executables:
     - samtools
   type: recipe
-install_config_file:
+container_config_file:
   associated_recipe:
     - mip
   data_type: SCALAR
@@ -371,6 +389,8 @@ recipe_core_number:
     genomic_superdups: 1
     giab: 1
     gnomad: 1
+    gnomad_chrsplit: 13
+    gnomad_mt: 1
     gnomad_pli_per_gene: 1
     hapmap: 1
     human_reference: 1
@@ -423,6 +443,8 @@ recipe_time:
     genomic_superdups: 1
     giab: 1
     gnomad: 25
+    gnomad_chrsplit: 32
+    gnomad_mt: 1
     gnomad_pli_per_gene: 1
     hapmap: 1
     human_reference: 1

definitions/dragen_rd_dna_parameters.yaml

@@ -8,7 +8,7 @@ custom_default_parameters:
     - conda_path
     - exome_target_bed
     - infile_dirs
-    - install_config_file
+    - container_config_file
     - pedigree_fam_file
     - picardtools_path
     - reference_dir
@@ -194,13 +194,13 @@ sv_annotate:
     - bcftools
     - svdb
   type: recipe
-sv_fqa_annotations:
+sv_fqa_vcfanno_filters:
   associated_recipe:
     - sv_annotate
   data_type: ARRAY
   default:
     - GNOMADAF
-    - GNOMADAF_POPMAX
+    - GNOMADAF_popmax
   type: recipe_argument
 sv_bcftools_view_filter:
   associated_recipe:
@@ -530,7 +530,7 @@ fqf_bcftools_filter_threshold:
   associated_recipe:
     - frequency_filter
   data_type: SCALAR
-  default: 0.40
+  default: 0.70
   type: recipe_argument
 cadd_ar:
   analysis_mode: case