Update busco to v4.1.3

containers/busco/Dockerfile

@@ -0,0 +1,21 @@
+FROM nfcore/base:1.10.2
+LABEL authors="Hadrien Gourlé <hadrien.gourle@slu.se>, Daniel Straub <d4straub@gmail.com>, Sabrina Krakau <sabrinakrakau@gmail.com>" \
+      description="Docker image containing BUSCO requirements for the nf-core/mag pipeline"
+
+# Install the conda environment
+COPY environment.yml /
+RUN conda env create --quiet -f /environment.yml && conda clean -a
+
+# For BUSCO to avoid segfault error with R 4.0.2
+RUN apt-get update
+RUN apt-get install -y libxt6
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-mag-busco-1.1.0dev/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-mag-busco-1.1.0dev > nf-core-mag-busco-1.1.0dev.yml
+
+# Instruct R processes to use these empty files instead of clashing with a local version
+RUN touch .Rprofile
+RUN touch .Renviron

containers/busco/environment.yml

@@ -0,0 +1,21 @@
+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: nf-core-mag-busco-1.1.0dev
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::python=3.7.3
+  - bioconda::prodigal=2.6.3                      # fix versions of third-party tools used by busco to avoid problems
+  - bioconda::augustus=3.3.3
+  - bioconda::diamond=2.0.1
+  - bioconda::hmmer=3.1b2
+  - bioconda::blast=2.10.1
+  - bioconda::sepp=4.3.10
+  - conda-forge::cairo=1.16.0                     # to avoid segfault error with R 4.0.2
+  - conda-forge::r-rgtk2=2.20.36                  # same as above
+  - conda-forge::fonts-conda-ecosystem=1          # to avoid missing fonts in R (https://github.com/conda-forge/r-base-feedstock/issues/91)
+  - conda-forge::r-base=4.0.2                     # busco requires R >= 4
+  - conda-forge::r-ggplot2=3.3.2
+  - bioconda::busco=4.1.3

environment.yml

@@ -19,13 +19,12 @@ dependencies:
   - bioconda::bowtie2=2.3.5
   - bioconda::quast=5.0.2
   - bioconda::prodigal=2.6.3
-  - bioconda::diamond=0.9.24 # 0.9.25 conflicts with Busco over boost
+  - bioconda::diamond=0.9.24 # 0.9.25 conflicted with Busco over boost
   - conda-forge::r=3.6
   - conda-forge::biopython=1.74
   - bioconda::krona=2.7.1
   - conda-forge::r-markdown=1.0
   - conda-forge::r-ggplot2=3.2.0
-  - bioconda::busco=3.0.2
   - bioconda::nanoplot=1.26.3
   - bioconda::filtlong=0.2.0
   - bioconda::porechop=0.2.3_seqan2.1.1