35 lines
923 B
Markdown
35 lines
923 B
Markdown
# Workflow template
|
|
|
|
This repository contains a nextflow workflow template and associated
|
|
container build.
|
|
|
|
## Quickstart
|
|
|
|
```bash
|
|
# build the container
|
|
CONTAINER_TAG=template-workflow
|
|
docker build \
|
|
-t ${CONTAINER_TAG} -f Dockerfile \
|
|
--build-arg BASEIMAGE=epi2melabs/base-workflow-image:latest \
|
|
.
|
|
```
|
|
|
|
The `BASEIMAGE` argument here can be changed to use an alternative image.
|
|
|
|
|
|
The template includes a simple workflow that outputs a file with the lengths
|
|
of sequences contained in a .fastq.gz file.
|
|
```
|
|
# run the pipeline with the test data
|
|
OUTPUT=template-workflow
|
|
nextflow run workflow.nf \
|
|
-w ${OUTPUT}/workspace \
|
|
-profile standard \
|
|
--reads test_data/reads.fq.gz \
|
|
--out_dir ${OUTPUT}
|
|
```
|
|
|
|
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.
|