Add default containers for annotation

README.md

@@ -133,10 +133,9 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 * [CHANGELOG](CHANGELOG.md)
 
 ## Aknowledgements
-[<img src="docs/images/SciLifeLab_logo.png" alt="SciLifeLab logo" title="SciLifeLab" style="padding:20px;height:80px">][scilifelab-link]
-[<img src="docs/images/BTB_logo.png" alt="Barntumörbanken logo" title="Barntumörbanken" style="padding:20px;height:80px">][btb-link]
-[<img src="docs/images/NGI_logo.png" alt="National Genomics Infrastructure logo" title="National Genomics Infrastructure" style="padding:20px;height:80px">][ngi-link]
-[<img src="docs/images/NBIS_logo.png" alt="National Bioinformatics Infrastructure Sweden logo" title="National Bioinformatics Infrastructure Sweden" style="padding:20px;height:80px">][nbis-link]
+[![Barntumörbanken](docs/images/BTB_logo.png)](https://ki.se/forskning/barntumorbanken-0) | [![SciLifeLab](docs/images/SciLifeLab_logo.png)](https://scilifelab.se)
+:-:|:-:
+[![National Genomics Infrastructure](docs/images/NGI_logo.png)](https://ngisweden.scilifelab.se/) | [![National Bioinformatics Infrastructure Sweden](docs/images/NBIS_logo.png)](https://nbis.se)
 
 [bioconda-badge]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?logo=data:image/png;base64,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
 [btb-link]: https://ki.se/forskning/barntumorbanken-0

containers/snpeff/Dockerfile

@@ -0,0 +1,17 @@
+FROM nfcore/base:latest
+
+LABEL \
+  author="Maxime Garcia" \
+  description="snpEff image for use in nf-core/sarek" \
+  maintainer="maxime.garcia@scilifelab.se"
+
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/sarek-snpeff-2.5dev/bin:$PATH
+
+# Setup default ARG variables
+ARG CACHE_VERSION=86
+ARG GENOME=GRCh38
+
+# Download Genome
+RUN snpEff download -v ${GENOME}.{CACHE_VERSION}

containers/snpeff/environment.yml

@@ -0,0 +1,10 @@
+# You can use this file to create a conda environment for this pipeline:
+# conda env create -f environment.yml
+name: sarek-snpeff-2.5dev
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - snpeff=4.3.1t

containers/vep/Dockerfile

@@ -0,0 +1,26 @@
+FROM nfcore/base:latest
+
+LABEL \
+  author="Maxime Garcia" \
+  description="VEP image for use in nf-core/sarek" \
+  maintainer="maxime.garcia@scilifelab.se"
+
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/sarek-vep-2.5dev/bin:$PATH
+
+# Setup default ARG variables
+ARG GENOME=GRCh38
+ARG SPECIES=homo_sapiens
+ARG VEP_VERSION=95
+
+# Download Genome
+RUN vep_install \
+  -a c \
+  -c .vep \
+  -s ${SPECIES} \
+  -v ${VEP_VERSION} \
+  -y ${GENOME} \
+  --CACHE_VERSION ${VEP_VERSION} \
+  --CONVERT \
+  --NO_HTSLIB --NO_TEST --NO_BIOPERL --NO_UPDATE

containers/vep/environment.yml

@@ -0,0 +1,11 @@
+# You can use this file to create a conda environment for this pipeline:
+# conda env create -f environment.yml
+name: sarek-vep-2.5dev
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - ensembl-vep=95.2
+  - genesplicer=1.0