{% if page.title %}{{ page.title }}{% endif %}{% if page.title and site.title %} – {% endif %}{% if site.title %}{{ site.title }}{% endif %} -

+{% tabs input %} +{% tab input generic %} +main-input.yaml ``` fq: class: File @@ -54,13 +57,40 @@ 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 } + +{% endtab %} + +{% tab input arvados %} +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: 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 } +{% endtab %} +{% endtabs %} +

+{% tabs output %} + +{% tab output generic %} ``` { "bam_sorted_indexed": { @@ -156,6 +194,36 @@ The CWL runner will print a results JSON object to standard output. It will loo } ``` {: .language-yaml } +{% endtab %} + +{% tab output arvados %} +``` +{ + "bam_sorted_indexed": { + "basename": "Aligned.sortedByCoord.out.bam", + "class": "File", + "location": "keep:2dbaaef5aefd558e37f14280e47091a9+327/Aligned.sortedByCoord.out.bam", + "secondaryFiles": [ + { + "basename": "Aligned.sortedByCoord.out.bam.bai", + "class": "File", + "location": "keep:2dbaaef5aefd558e37f14280e47091a9+327/Aligned.sortedByCoord.out.bam.bai" + } + ], + "size": 25370695 + }, + "qc_html": { + "basename": "Mov10_oe_1.subset_fastqc.html", + "class": "File", + "location": "keep:2dbaaef5aefd558e37f14280e47091a9+327/Mov10_oe_1.subset_fastqc.html", + "size": 383589 + } +} +``` +{: .language-yaml } +{% endtab %} +{% endtabs %} +

+{% tabs setup %} +{% tab setup generic %} + # Setting up a practice repository We will create a new git repository and import a library of existing tool definitions that will help us build our workflow. -Create a new git repository to hold our workflow with this command: +Create a new empty git repository to hold our workflow with this command: ``` git init rnaseq-cwl-training-exercises ``` - -On Arvados use this: - -``` -git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises -``` +{: .language-bash } Next, import bio-cwl-tools with this command: ``` git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git ``` +{: .language-bash } # Downloading sample and reference data @@ -32,8 +32,9 @@ Start from your rnaseq-cwl-exercises directory. ``` mkdir rnaseq cd rnaseq -wget --mirror --no-parent --no-host --cut-dirs=1 https://download.pirca.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/ +wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/ ``` +{: .language-bash } # Downloading or generating STAR index @@ -46,8 +47,9 @@ This is a rather large download (4 GB). Depending on your bandwidth, it may be ``` mkdir hg19-chr1-STAR-index cd hg19-chr1-STAR-index -wget --mirror --no-parent --no-host --cut-dirs=1 https://download.pirca.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/ +wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/ ``` +{: .language-bash } ## Generating @@ -64,12 +66,101 @@ Gtf: location: rnaseq/reference_data/chr1-hg19_genes.gtf Overhang: 99 ``` +{: .language-yaml } Generate the index with your local cwl-runner. ``` cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml ``` +{: .language-bash } + + +{% endtab %} + +{% tab setup arvados %} + +# Setting up a practice repository + +We will create a new git repository and import a library of existing +tool definitions that will help us build our workflow. + +When using the recommended VSCode environment to develop on Arvados, start by forking this repository: +``` +git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises +``` +{: .language-bash } + +Next, import bio-cwl-tools with this command: + +``` +git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git +``` +{: .language-bash } + +# Downloading sample and reference data + +> ## Note +> +> You may already have access to this collection. +> +> You can check by going to Workbench and pasting +> `9178fe1b80a08a422dbe02adfd439764+925` into the search box. If you +> arrived at a collection page instead of a "not found" error, then +> you do not need to perform this download step. +{: .callout} + +``` +arv-copy --src jutro 9178fe1b80a08a422dbe02adfd439764+925 +``` +{: .language-bash } + +# Downloading or generating STAR index + +Running STAR requires index files generated from the reference. + +This is a rather large download (4 GB). Depending on your bandwidth, it may be faster to generate it yourself. + +## Downloading + +> ## Note +> +> As above, you can check by going to Workbench and pasting +> `02a12ce9e2707610991bd29d38796b57+2912` into the search box to see +> if you already have access to this collection. +{: .callout} + +``` +arv-copy --src jutro 02a12ce9e2707610991bd29d38796b57+2912 +``` +{: .language-bash } + +## Generating + +Create `chr1-star-index.yaml`: + +``` +InputFiles: + - class: File + location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1.fa + format: http://edamontology.org/format_1930 +IndexName: 'hg19-chr1-STAR-index' +Gtf: + class: File + location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf +Overhang: 99 +``` +{: .language-yaml } + +Generate the index with arvados-cwl-runner. + +``` +arvados-cwl-runner bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml +``` +{: .language-bash } +{% endtab %} +{% endtabs %} +