Containerized

runAnnotation/Dockerfile

@@ -0,0 +1,47 @@
+# syntax=docker/dockerfile:1
+FROM continuumio/miniconda3:24.5.0-0 AS build
+
+ENV container=docker
+
+# add conda channels
+RUN conda config --add channels conda-forge \
+    && conda config --add channels bioconda
+
+RUN conda init bash \
+    && . ~/.bashrc \
+    && conda create --name annotation \
+    && conda activate annotation 
+
+RUN conda install -n annotation -c bioconda perl-lwp-protocol-https
+RUN conda install -n annotation -c conda-forge r-base
+RUN conda install -n annotation -c bioconda prokka
+RUN conda install -n annotation -c bioconda mummer
+RUN conda install -n annotation -c bioconda blast=2.16
+RUN conda install -n annotation -c bioconda perl-yaml
+
+RUN conda install -c conda-forge conda-pack
+
+#Custom implementation of RATT from EDGE
+RUN wget https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_thirdParty_softwares.tgz \
+    && tar -xvzf edge_dev_thirdParty_softwares.tgz \
+    && tar -xvzf thirdParty/RATT.tar.gz -C . \
+    && mv RATT /opt/conda/envs/annotation/opt
+
+#add scripts from this project to bin
+ADD bin/* /opt/conda/envs/annotation/bin
+
+#pack environment for runtime image
+RUN conda-pack -n annotation -o /tmp/env.tar && \
+    mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
+    rm /tmp/env.tar
+
+RUN /venv/bin/conda-unpack
+
+FROM debian:latest AS runtime
+
+COPY --from=build /venv /venv
+
+ENV PATH=/venv/bin:/venv/opt/RATT:$PATH
+
+SHELL ["/bin/bash", "-c"]
+CMD /bin/bash

runAnnotation/bin/runRATT.sh

@@ -1,5 +1,6 @@
 #!/bin/bash
 
-export RATT_HOME=$CONDA_PREFIX/opt/RATT #remove when Dockerizeing
+#this is the correct location in this workflow's container
+export RATT_HOME=/venv/opt/RATT #remove when Dockerizeing
 
 $RATT_HOME/start.ratt.sh $1 $2 $3 $4

runAnnotation/nextflow.config

@@ -14,6 +14,12 @@ params {
 
 }
 
+singularity {
+    enabled=true
+    runOptions="--compat --bind .:/venv/bin/ec_info"
+}
+process.container = 'apwat/annotation:0.4'
+
 workflow.onComplete = {
     "rm -rf nf_assets".execute().text
 }

runAnnotation/runAnnotation.nf

@@ -123,7 +123,6 @@ process annPlot {
     path "plot_gff3.log"
     path "annotation_stats_plots.pdf"
     path "${params.projName}.txt", optional:true
-    //see what goes missing if we only publish that
 
     script:
     def rattReport = params.annotateProgram.equalsIgnoreCase("ratt") ? "awk \'\$1 ~ /CDS|RNA/ {print \$1\": \"\$2}' plot_gff3.log > ${params.projName}.txt" : ""