As a testing tool, we use gh-trs or yevis-cli.
All workflows introduced in the book has been translated in CWL, but yet the testing is ongoing.
- Animal genome assembly by inutano
- WIP
- Bacteria genome by suecharo
- bacteria_genome
- Disease genome by tom-tan
- WIP
- Epigenome: Bisulfite-Seq by manabuishii
- download_rawdata
- download_reference_fasta
- bismark_genome_preparation_workflow
- epigenome-BS-seq
- fastqc-workflow
- Epigenome: ChIP-Seq by suecharo
- WIP
- Meta 16S-Seq by inutano
- meta16s-seq.demo
- RNA-seq by ykohki
- rnaseq-1sample-kallisto-pe
- rnaseq-1sample-star-rsem-pe
- rnaseq-deseq2_gene
- rnaseq-kallisto-pe
- rnaseq-kallisto-sleuth
- rnaseq-sleuth_isoform
- rnaseq-star_index
- rnaseq-star-rsem-deseq2
- rnaseq-star-rsem-tar-pe
- rnaseq-star-rsem-pe
- Transcriptome assembly by yyoshiaki
- transcriptome_assemble
As an example, use tool/cat/cat.cwl.
If tests are prepared, yevis-metadata.yml exists in the same directory.
Using gh-trs and yevis-metadata.yml, run the test as follows:
$ gh-trs ./tool/cat/yevis-metadata.yml
# or
$ gh-trs https://raw.githubusercontent.com/ddbj/yevis-cli/main/tool/cat/yevis-metadata.ymlAs a CI using GitHub Actions, action files are available under .github/workflows with a prefix test-tool.
The event handlers for each action are as follows:
on:
push:
branches:
- main
paths:
- "tool/cat/**"
schedule:
- cron: "00 04 1 */6 *"
workflow_dispatch: {}To run all tests, use run_all_tool_tests_with_gh_actions.sh as follows:
$ bash run_all_tool_tests_with_gh_actions.shThe test status by GitHub Actions is as follows:
