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Build pipeline: viash-hub.htrnaseq.update-readme-km2t9
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86 lines
3.9 KiB
Plaintext
---
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format: gfm
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---
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```{r setup, include=FALSE}
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project <- yaml::read_yaml("_viash.yaml")
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license <- paste0(project$links$repository, "/blob/main/LICENSE")
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contributing <- paste0(project$links$repository, "/blob/main/CONTRIBUTING.md")
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```
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# HT-RNAseq
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[](https://www.viash-hub.com/packages/`r project$name`)
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[](`r project$links$repository`)
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[](`r license`)
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[](`r project$links$issue_tracker`)
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[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue)](https://viash.io)
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## Introduction
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`r project$description`
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## Example usage
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## Test and example data
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If you want to explore this workflow, it's possible to the use data we use as test data: [a DRUGseq dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176150) from the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra). For the unit and integration tests, this data has been (partly) subsampled to reduce the test runtime. We used [seqtk](https://github.com/lh3/seqtk) for this with a seed of 1, e.g.:
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```bash
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seqtk sample -s1 orig/SRR14730302/VH02001614_S8_R1_001.fastq.gz 10000 > 10k/SRR14730302/VH02001614_S8_R1_001.fastq.gz
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```
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This data is available at: `gs://viash-hub-test-data/htrnaseq/v1/`.
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## Run from Viash Hub
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Open [Viash Hub](https://www.viash-hub.com) and browse to the [htrnaseq component](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq). Press the 'Launch' button and follow the instructions.
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We will start an example run loading just one input and using a barcodes fast file containing only 2 wells.
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In the first step, we add the `local` profile to the list of profiles in order to the cpu and memory requirements of the workflow steps:
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In the next step, we provide the paramters as follows:
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- `input_r1`: `gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R1_001.fastq`
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- `input_r2`: `gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R2_001.fastq`
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- `genomeDir`: `gs://viash-hub-test-data/htrnaseq/v1/genomeDir/subset/Homo_sapiens/v0.0.3/`
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- `barcodesFasta`: `gs://viash-hub-test-data/htrnaseq/v1/2-wells-with-ids.fasta`
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- `annotation`: `gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.annotation.gtf.gz`
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Please not the following: Both `input_r1` and `input_r2` take multiple values. This means that one has to press ENTER after pasting the input path.
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Press the 'Launch' button at the end to get the instructions on how to run the workflow from the CLI.
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## Run using NF-Tower / Seqera Cloud
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It's possible to run the workflow directly from Seqera Cloud. The necessary schema file has been built and provided with the workflows in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters when using the form -based input.
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It's better to use Viash Hub also here:
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First, 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, you will get the option to select a 'Workspace' and a 'Compute environment'.
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Next, we need to fill in the paramters for the run. This is similar to before:
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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.
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# Contributions
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Developed in collaboration with Data Intuitive and Open Analytics.
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Other contributions are welcome.
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