.gitlab-ci.yml

@@ -7,12 +7,36 @@ image: ${IMAGE}
 variables:
     BASEIMAGE: ${CI_REGISTRY}/${CURRENT_TEMPLATE_IMAGE}
 
+.install-nextflow: &install-nextflow |
+    wget -qO- https://get.nextflow.io | bash
+
+.install-conda: &install-conda |
+    wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p ./miniconda
+    source ./miniconda/bin/activate
+    conda init
+    
+
+conda-run:
+    image: ubuntu:20.04
+    stage: build_and_run
+    before_script:
+        - apt update && apt install -y wget default-jre
+        - *install-nextflow
+        - *install-conda
+    script:
+        - ./nextflow run workflow.nf
+              -w ${OUTPUT}/workspace
+              -profile conda
+              --reads test_data/reads.fq.gz 
+              --out_dir ${OUTPUT}
+
+
 build-image:
     stage: build_and_run
-    variables:
     before_script:
         - apk add wget openjdk11 bash
-        - wget -qO- https://get.nextflow.io | bash
+        - *install-nextflow
     script:
         - echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
         - TAG="${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}"

Dockerfile

@@ -1,13 +1,13 @@
 ARG BASEIMAGE=epi2melabs/base-workflow-image:latest
 FROM $BASEIMAGE
 
-# Minimal install for example purposes 
+# Minimal install for example purposes
+COPY environment.yaml $HOME/environment.yaml 
 RUN \
     . $CONDA_DIR/etc/profile.d/mamba.sh \
-    && micromamba activate \ 
-    && micromamba install -y \
-            pysam \
-        -c anaconda -c conda-forge -c bioconda -q -y \
+    && micromamba activate \
+    && micromamba install --help \
+    && micromamba install --file $HOME/environment.yaml \
     && fix-permissions $CONDA_DIR \
     && fix-permissions $HOME
 

README.md

@@ -1,12 +1,19 @@
 # Workflow template
 
-This repository contains a nextflow workflow template and associated
-container build.
+This repository contains a Nextflow workflow template and associated Docker
+container build. The workflow also supports using conda environments as an
+alternative software isolation method to Docker.
 
 ## Quickstart
 
+### Building the container
+
+> This step is not necessary if you intend to run the workflow using
+> conda environments.
+
+The Docker container image can be built with the following command:
+
 ```bash
-# build the container
 CONTAINER_TAG=template-workflow
 docker build \
     -t ${CONTAINER_TAG} -f Dockerfile \
@@ -16,11 +23,17 @@ docker build \
 
 The `BASEIMAGE` argument here can be changed to use an alternative image.
 
+### Running the workflow
 
 The template includes a simple workflow that outputs a file with the lengths
 of sequences contained in a .fastq.gz file.
+
+**Running the workflow with Docker containers**
+
+To run the workflow using Docker containers supply the `-profile standard`
+argument to `nextflow run`:
+
 ```
-# run the pipeline with the test data
 OUTPUT=template-workflow
 nextflow run workflow.nf \
     -w ${OUTPUT}/workspace \
@@ -32,3 +45,25 @@ nextflow run workflow.nf \
 The output of the pipeline will be found in `./template-workflow` for the above
 example. This directory contains the nextflow working directories alongside
 the two primary outputs of the pipeline.
+
+**Using conda environments**
+
+To run the workflow backed by conda environments, simply provide the
+`-profile conda` argument to `nextflow run`.
+
+```
+# run the pipeline with the test data
+OUTPUT=template-workflow
+nextflow run workflow.nf \
+    -w ${OUTPUT}/workspace \
+    -profile conda \
+    --reads test_data/reads.fq.gz \
+    --out_dir ${OUTPUT}
+```
+
+This will create a conda environment with all required software within the
+workspace directory. When running multiple analyses on distinct datasets
+it may not be desirable to have Nextflow create a conda environment for each
+analysis. To avoid the situation editing the file `nextflow.config` will
+be necessary. Search for the term `cacheDir` and set this to a directory
+where you wish the conda environment to be placed.

environment.yaml

@@ -0,0 +1,7 @@
+name: epi2melabs-nf-template-workflow
+channels:
+    - bioconda
+    - conda-forge
+    - defaults
+dependencies:
+    - pysam

nextflow.config

@@ -1,3 +1,14 @@
+//
+// Notes to End Users.
+//
+// The workflow should run without editing this configuration file,
+// however there may be instances in which you wish to edit this
+// file for compute performance or other reasons. Please see:
+// 
+//   https://nextflow.io/docs/latest/config.html#configuration
+//
+// for further help editing this file.
+
 
 process {
     withLabel:containerCPU {
@@ -16,4 +27,18 @@ profiles {
             runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
         }
     }
+
+    // profile using conda environments rather than docker
+    // containers
+    conda {
+        docker {
+            enabled = false
+        }
+        process {
+            conda = "environment.yaml"
+        }
+        conda {
+             cacheDir = ""
+        }
+    }
 }