Demultiplex.vsh is a workflow for demultiplexing of raw sequencing data. Currently data from Illumina and Element Biosciences sequencers are supported.
This workflow is designed to demultiplex raw RNA-seq sequencing data from Illumina and Element Biosciences sequencers.
The workflow is built in a modular fashion, where most of the base functionality is provided by components from
[`biobox`](https://www.viash-hub.com/packages/biobox/latest) supplemented by custom base components and workflow components in this package. Each of these components can be used independently as stand-alone modules with a
where a number of choices (input/output structure and location) have
been made.
## Workflow Overview
The workflow executes the following steps:
1. Unpacking the input data (when a TAR archive is provided)
2. Run `bclconvert` or `bases2fastq`
3. Run `falco` and convert Illumina InterOp information to csv
4. Run `multiqc` to generate a report
## Example usage
Two variants of the same workflow are provided, depending on the flexibility in the ouput structure required:
* The `runner` workflow provides a predifined output structure. It requires the minimal amount of parameters to be provided, at the cost of being less flexible. It is located at `target/nextflow/runner/main.nf`
* The `demultiplex` workflow (`target/nextflow/demultiplex/main.nf`) allows for more fine-grained tuning, but required more parameters to be provided.
### Test data
We have provided test data at `gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2` (Illumina), but please feel free to bring your own. The URL of the test data can be provided as-is to the workflow, or you can download everything and specify a local path.
The input data should follow the structure of either Illumina or Element Biosciences sequencers. The workflow will automatically detect which demultiplexer to use (`bclconvert` or `bases2fastq`) based on the
presence of either `SampleSheet.csv` or `RunParameters.xml` in the input directory. Demultiplexer can also be set explicitly using the `--demultiplexer` parameter.
### Setup
In order to use the workflows in this package, you'll need to do the following:
has been built and provided with the workflows in order to use the
form-based input.
1. Select the option to run the workflow using Seqera Cloud. You
will need to create an API token for your account. Once this token is
filled in in the corresponding field, we will get the option to select
a ‘Workspace’ and a ‘Compute environment’.
2. Provide the parameters similar to the previous step.
3. In the next screen, pressing the ‘Launch’ button will actually start the
workflow on Seqera Cloud. A message is shown when the submit was
successful.
### Setting up SCM
In order to let nextflow use the viash-hub workflows, you need to setup a [SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) file. This can be done once by creating `$HOME/.nextflow/scm` and adding the following:
```
providers {
vsh {
platform = 'gitlab'
server = "packages.viash-hub.com"
}
}
```
Alternatively, a custom location for the SCM file can be specified using the `NXF_SCM_FILE` environment variable.
You can check if everything is working by getting the `--help` for a workflow:
Nextflow's labels can be used to specify the amount of resources a process can use. This workflow uses the following labels for CPU and memory:
* `verylowmem`, `lowmem`, `midmem`, `highmem`
* `verylowcpu`, `lowcpu`, `midcpu`, `highcpu`
The defaults for these labels can be found at `src/config/labels.config`. Nextflow checks that the specified resources for a process do not exceed what is available on the machine and will not start if it does. Create your own config file to tune the labels to your needs, for example:
```
// Resource labels
withLabel: verylowcpu { cpus = 2 }
withLabel: lowcpu { cpus = 8 }
withLabel: midcpu { cpus = 16 }
withLabel: highcpu { cpus = 16 }
withLabel: verylowmem { memory = 4.GB }
withLabel: lowmem { memory = 8.GB }
withLabel: midmem { memory = 8.GB }
withLabel: highmem { memory = 8.GB }
```
When starting nextflow using the CLI, you can use `-c` to provide the file to nextflow and overwrite the defaults.
## Acknowledgements
Developed in collaboration with Data Intuitive and Open Analytics.
