34 lines
2.2 KiB
Markdown
34 lines
2.2 KiB
Markdown
These are instructions to install and run the workflow on command line. You can also access the workflow via the [EPI2ME application](https://labs.epi2me.io/downloads/).
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The workflow uses [Nextflow](https://www.nextflow.io/) to manage compute and software resources, therefore nextflow will need to be installed before attempting to run the workflow.
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The workflow can currently be run using either [Docker](https://www.docker.com/products/docker-desktop) or
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[Singularity](https://docs.sylabs.io/guides/3.0/user-guide/index.html) to provide isolation of
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the required software. Both methods are automated out-of-the-box provided
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either docker or singularity is installed. This is controlled by the [`-profile`](https://www.nextflow.io/docs/latest/config.html#config-profiles) parameter as exemplified below.
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It is not required to clone or download the git repository in order to run the workflow.
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More information on running EPI2ME workflows can be found on our [website](https://labs.epi2me.io/wfindex).
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The following command can be used to obtain the workflow. This will pull the repository in to the assets folder of nextflow and provide a list of all parameters 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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A demo dataset is provided for testing of the workflow. It can be downloaded using:
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```
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wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz
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tar -xzvf differential_expression.tar.gz
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```
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The workflow can be run with the demo data using:
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```
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nextflow run epi2me-labs/wf-transcriptome \
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--fastq differential_expression/differential_expression_fastq \
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--de_analysis --ref_genome differential_expression/hg38_chr20.fa \
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--transcriptome-source reference-guided \
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--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
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--direct_rna --minimap2_index_opts '-k 15' --sample_sheet differential_expression/sample_sheet.csv \
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--jaffal_refBase differential_expression/chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22 \
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-profile standard
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```
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For further information about running a workflow on the cmd line see https://labs.epi2me.io/wfquickstart/ |