Wrapped BioWardrobe's CWL files
CWL workflows for BioWardrobe project. This package includes all the original BioWardrobe's pipelines, simplifies import for biowardrobe-airflow-analysis. It also includes extra pipelines for new project SciDAP.
pip3 install biowardrobe-cwl-workflows
or from sources
git clone https://github.com/datirium/workflows pip3 install .
from biowardrobe_cwl_workflows import available _path_to_workflow=available(workflow='chipseq-se.cwl')
Extra features in CWL
Metadata & Upstreams
'sd:metadata': - "../metadata/chipseq-header.cwl" 'sd:upstream': genome_indices: "genome-indices.cwl" control_file: "chipseq-se.cwl"
To enable users to extend user interface (dynamic form) with extra input fields not required by a workflow
'sd:metadata' field were introduced. It defines a list of workflows where inputs field just used for constructing and storing the input object.
To simplify selection of already analyzed common data
’sd:upstream’ were introduced. It defines the upstream workflows of the process. The process is ready to run when upstream output data is available.
Example of extra input fields for user interface:
cwlVersion: v1.0 class: Workflow inputs: cells: type: string label: "Cells" sd:preview: position: 1 conditions: type: string label: "Conditions" sd:preview: position: 3 alias: type: string label: "Experiment short name/Alias" sd:preview: position: 2 catalog: type: string? label: "Catalog #" description: type: string? 'sd:type': 'text' label: "Description" outputs:  steps: 
CWL VisualPlugins for output data
outputs: ... fastx_statistics: type: File label: "FASTQ statistics" format: "http://edamontology.org/format_2330" doc: "fastx_quality_stats generated FASTQ file quality statistics file" outputSource: fastx_quality_stats/statistics_file 'sd:visualPlugins': - line: Title: 'Base frequency plot' xAxisTitle: 'Nucleotide position' yAxisTitle: 'Frequency' colors: ["#b3de69", "#99c0db", "#fb8072", "#fdc381", "#888888"] data: [$12, $13, $14, $15, $16] ...
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