X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/blobdiff_plain/cc20b244789bda85dece42ae01db9739eda2b192..2f8029fae95be67664dde4e8c40d7ef15fd64631:/_episodes/03-running.md diff --git a/_episodes/03-running.md b/_episodes/03-running.md index ba37ad3..9c62714 100644 --- a/_episodes/03-running.md +++ b/_episodes/03-running.md @@ -31,8 +31,8 @@ plain strings that may or may not be file paths. Note: if you don't have example sequence data or the STAR index files, see [setup](/setup.html). +{% capture generic_input_tab_content %} main-input.yaml - ``` fq: class: File @@ -54,13 +54,47 @@ gtf: > ``` > cwl-runner main.cwl main-input.yaml > ``` +> {: .language-bash } > > This may take a few minutes to run, and will print some amount of > logging. The logging you see, how access other logs, and how to > track workflow progress will depend on your CWL runner platform. +{: .challenge } +{% endcapture %} + +{% capture arvados_input_tab_content %} +main-input.yaml +``` +fq: + class: File + location: keep:9178fe1b80a08a422dbe02adfd439764+925/raw_fastq/Mov10_oe_1.subset.fq + format: http://edamontology.org/format_1930 +genome: + class: Directory + location: keep:02a12ce9e2707610991bd29d38796b57+2912 +gtf: + class: File + location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf +``` +{: .language-yaml } + +> ## Running the workflow +> +> If you are using VSCode with Arvados tasks, select `main.cwl` and +> then use the `Run CWL Workflow on Arvados` task. > -> {: .language-bash } {: .challenge } +{% endcapture %} + +