61 lines
2.2 KiB
Markdown
61 lines
2.2 KiB
Markdown
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These are instructions to install and run the workflow on command line.
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You can also access the workflow via the
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[EPI2ME Desktop application](https://labs.epi2me.io/downloads/).
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The workflow uses [Nextflow](https://www.nextflow.io/) to manage
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compute and software resources,
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therefore Nextflow will need to be
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installed before attempting to run the workflow.
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The workflow can currently be run using either
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[Docker](https://www.docker.com/products/docker-desktop)
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or [Singularity](https://docs.sylabs.io/guides/3.0/user-guide/index.html)
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to provide isolation of the required software.
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Both methods are automated out-of-the-box provided
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either Docker or Singularity is installed.
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This is controlled by the
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[`-profile`](https://www.nextflow.io/docs/latest/config.html#config-profiles)
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parameter as exemplified below.
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It is not required to clone or download the git repository
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in order to run the workflow.
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More information on running EPI2ME workflows can
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be found on our [website](https://labs.epi2me.io/wfindex).
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The following command can be used to obtain the workflow.
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This will pull the repository in to the assets folder of
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Nextflow and provide a list of all parameters
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available for the workflow as well as an example command:
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```
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nextflow run epi2me-labs/wf-transcriptomes --help
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```
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To update a workflow to the latest version on the command line use
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the following command:
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```
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nextflow pull epi2me-labs/wf-transcriptomes
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```
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A demo dataset is provided for testing of the workflow.
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It can be downloaded and unpacked using the following commands:
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```
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wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/wf-transcriptomes-demo.tar.gz
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tar -xzvf wf-transcriptomes-demo.tar.gz
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```
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The workflow can then be run with the downloaded demo data using:
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```
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nextflow run epi2me-labs/wf-transcriptomes \
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--de_analysis \
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--direct_rna \
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--fastq 'wf-transcriptomes-demo/differential_expression_fastq' \
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--minimap2_index_opts '-k15' \
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--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \
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--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \
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--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
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-profile standard
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```
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For further information about running a workflow on
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the command line see https://labs.epi2me.io/wfquickstart/
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