72 lines
2.2 KiB
Markdown
72 lines
2.2 KiB
Markdown
# Workflow template
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This repository contains a Nextflow workflow template and associated Docker
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container build. The workflow also supports using conda environments as an
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alternative software isolation method to Docker.
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## Quickstart
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### Building the container
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> This step is not necessary if you intend to run the workflow using
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> conda environments, or are not interesting in developing of modifying
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> the workflow. The current release version of the container is located
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> on dockerhub with the tag ontresearch/wf-template.
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The Docker container image can be built with the following command:
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```bash
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CONTAINER_TAG=ontresearch/wf-template
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docker build \
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-t ${CONTAINER_TAG} -f Dockerfile \
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--build-arg BASEIMAGE=ontresearch/base-workflow-image:v0.1.0 \
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.
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```
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The `BASEIMAGE` argument here can be changed to use an alternative image.
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### Running the workflow
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The template includes a simple workflow that outputs a file with the lengths
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of sequences contained in a .fastq.gz file.
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**Running the workflow with Docker containers**
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To run the workflow using Docker containers supply the `-profile standard`
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argument to `nextflow run`:
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```
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OUTPUT=workflow-output
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nextflow run main.nf \
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-w ${OUTPUT}/workspace \
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-profile standard \
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--fastq test_data/reads.fq.gz \
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--out_dir ${OUTPUT}
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```
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The output of the pipeline will be found in `./workflow-output` for the above
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example. This directory contains the nextflow working directories alongside
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the two primary outputs of the pipeline.
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**Using conda environments**
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To run the workflow backed by conda environments, simply provide the
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`-profile conda` argument to `nextflow run`.
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```
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# run the pipeline with the test data
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OUTPUT=workflow-output
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nextflow run main.nf \
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-w ${OUTPUT}/workspace \
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-profile conda \
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--fastq test_data/reads.fq.gz \
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--out_dir ${OUTPUT}
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```
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This will create a conda environment with all required software within the
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workspace directory. When running multiple analyses on distinct datasets
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it may not be desirable to have Nextflow create a conda environment for each
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analysis. To avoid the situation editing the file `nextflow.config` will
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be necessary. Search for the term `cacheDir` and set this to a directory
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where you wish the conda environment to be placed.
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