kfukuta/wf-transcriptomes-v202
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Minor edits to readme

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Chris Wright 2021-03-01 10:32:51 +00:00
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README.md
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@ -9,12 +9,14 @@ alternative software isolation method to Docker.
### Building the container ### Building the container
> This step is not necessary if you intend to run the workflow using > This step is not necessary if you intend to run the workflow using
> conda environments. > conda environments, or are not interesting in developing of modifying
> the workflow. The current release version of the container is located
> on dockerhub with the tag ontresearch/wf-template.
The Docker container image can be built with the following command: The Docker container image can be built with the following command:
```bash ```bash
CONTAINER_TAG=ontresearch/template-workflow CONTAINER_TAG=ontresearch/wf-template
docker build \ docker build \
-t ${CONTAINER_TAG} -f Dockerfile \ -t ${CONTAINER_TAG} -f Dockerfile \
--build-arg BASEIMAGE=ontresearch/base-workflow-image:v0.1.0 \ --build-arg BASEIMAGE=ontresearch/base-workflow-image:v0.1.0 \
@ -34,15 +36,15 @@ To run the workflow using Docker containers supply the `-profile standard`
argument to `nextflow run`: argument to `nextflow run`:
``` ```
OUTPUT=template-workflow OUTPUT=workflow-output
nextflow run workflow.nf \ nextflow run main.nf \
-w ${OUTPUT}/workspace \ -w ${OUTPUT}/workspace \
-profile standard \ -profile standard \
--reads test_data/reads.fq.gz \ --reads test_data/reads.fq.gz \
--out_dir ${OUTPUT} --out_dir ${OUTPUT}
``` ```
The output of the pipeline will be found in `./template-workflow` for the above The output of the pipeline will be found in `./workflow-output` for the above
example. This directory contains the nextflow working directories alongside example. This directory contains the nextflow working directories alongside
the two primary outputs of the pipeline. the two primary outputs of the pipeline.
@ -53,8 +55,8 @@ To run the workflow backed by conda environments, simply provide the
``` ```
# run the pipeline with the test data # run the pipeline with the test data
OUTPUT=template-workflow OUTPUT=workflow-output
nextflow run workflow.nf \ nextflow run main.nf \
-w ${OUTPUT}/workspace \ -w ${OUTPUT}/workspace \
-profile conda \ -profile conda \
--reads test_data/reads.fq.gz \ --reads test_data/reads.fq.gz \