Datasets
Most bioinformatics pipelines require an input of some sort. This is typically a samplesheet where each row consists of a sample, the location of files for that sample (such as fastq files), and other sample details.
In the cloud, users may need to upload this samplesheet to a bucket or retrieve the path to this file on a shared filesystem to use it as pipeline input.
Instead, these samplesheets can be made easily accessible through the Datasets feature in Platform. Datasets allow users to upload a structued CSV (Comma-Separated Values) or TSV (Tab-Separated Values) file to a workspace. They are then used as inputs to pipelines to simplify data management, minimize user data-input errors, and facilitate reproducible workflows.
1. Download the nf-core/rnaseq test samplesheet
The nf-core/rnaseq pipeline works with input datasets (samplesheets) containing sample names, fastq file locations, and indications of strandedness. The Seqera Community Showcase sample dataset for nf-core/rnaseq looks like this:
Example rnaseq dataset
| sample | fastq_1 | fastq_2 | strandedness |
|---|---|---|---|
| WT_REP1 | s3://nf-core-awsmegatests/rnaseq/... | s3://nf-core-awsmegatests/rnaseq/... | reverse |
| WT_REP1 | s3://nf-core-awsmegatests/rnaseq/... | s3://nf-core-awsmegatests/rnaseq/... | reverse |
| WT_REP2 | s3://nf-core-awsmegatests/rnaseq/... | s3://nf-core-awsmegatests/rnaseq/... | reverse |
| RAP1_UNINDUCED_REP1 | s3://nf-core-awsmegatests/rnaseq/... | reverse | |
| RAP1_UNINDUCED_REP2 | s3://nf-core-awsmegatests/rnaseq/... | reverse | |
| RAP1_UNINDUCED_REP2 | s3://nf-core-awsmegatests/rnaseq/... | reverse | |
| RAP1_IAA_30M_REP1 | s3://nf-core-awsmegatests/rnaseq/... | s3://nf-core-awsmegatests/rnaseq/... | reverse |
Download the nf-core/rnaseq samplesheet_test.csv provided in this repository to your computer.
2. Add the Dataset
From the Datasets tab, select Add Dataset.
Specify the following dataset details:
- A Name for the dataset, such as 'nf-core-rnaseq-test-dataset'
- A Description
- Select the First row as header option
- Select Upload file and browse to the CSV file downloaded from this repository. This CSV file specifies the paths to 7 small FASTQ files for a sub-sampled Yeast RNAseq dataset.
Notice the location of the files point to a path on S3. This could also be a path to a shared filesystem, if using an HPC compute environment. Using the path to the files, Nextflow will stage the files into the task working directory.
Note
Seqera Platform will not store any data used for analysis in pipelines. The datasets must include locations of data that is stored elsewhere, on the user's infrastructure.