ChIP-Seq, ATAC-Seq, CLIP-Seq, RNA-Seq CWL workflows for use in Scientific Data Analysis Platform (SciDAP) or in BioWardrobe project or standalone with cwltool.
All the original BioWardrobe's pipelines has been rewritten in CWL and new workflows has been added. The repository pulls automatically into SciDAP platform.
There are 4 additional references that can be given to a workflow for added compatability within SciDAP.
To extend user interface (dynamic form) with extra input fields not required by a workflow, the 'sd:metadata' field was introduced.
It defines a list of workflow templates where the inputs object is used for constructing and storing extra fields with an original workflow.
chipseq-header.cwl
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 #"
outputs: []
steps: []
and include file as sd:metadata
'sd:metadata':
- "../metadata/chipseq-header.cwl"To extend the SciDAP UI to allow for already analysed data the be selectable as inputs, we organize a graph of separate workflows. To link workflows we use ’sd:upstream’, which defines a list of upstream workflows who's outputs are accible by this workflow.
...
'sd:upstream':
rnaseq_sample_untreated:
- "rnaseq-se.cwl"
- "rnaseq-pe.cwl"
- "rnaseq-se-dutp.cwl"
- "rnaseq-pe-dutp.cwl"
- "rnaseq-se-dutp-mitochondrial.cwl"
- "rnaseq-pe-dutp-mitochondrial.cwl"
- "trim-rnaseq-pe.cwl"
- "trim-rnaseq-se.cwl"
- "trim-rnaseq-pe-dutp.cwl"
- "trim-rnaseq-se-dutp.cwl"
rnaseq_sample_treated:
- "rnaseq-se.cwl"
- "rnaseq-pe.cwl"
- "rnaseq-se-dutp.cwl"
- "rnaseq-pe-dutp.cwl"
- "rnaseq-se-dutp-mitochondrial.cwl"
- "rnaseq-pe-dutp-mitochondrial.cwl"
- "trim-rnaseq-pe.cwl"
- "trim-rnaseq-se.cwl"
- "trim-rnaseq-pe-dutp.cwl"
- "trim-rnaseq-se-dutp.cwl"
inputs:
untreated_files:
type: File[]
format:
- "http://edamontology.org/format_3752"
- "http://edamontology.org/format_3475"
label: "Untreated input CSV/TSV files"
doc: "Untreated input CSV/TSV files"
'sd:upstreamSource': "rnaseq_sample_untreated/rpkm_common_tss"
'sd:localLabel': true
...Usually, workflows' output results (especially files) are provided as download links in web interfaces. With SciDAP visualization plugins, data can be presented as a plot, as a genome browser, as a table, or (in the case of html outputs) to be opened in a new tab. The keyword 'sd:visualPlugins' enables SciDAP visualization plugins. line, pie, chart, igvbrowser, syncfusiongrid, and linkList types are already available in the platform.
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]
...
diff_expr_file:
type: File
label: "DESeq results, TSV"
format: "http://edamontology.org/format_3475"
doc: "DESeq generated list of differentially expressed items grouped by isoforms, genes or common TSS"
outputSource: deseq/diff_expr_file
'sd:visualPlugins':
- syncfusiongrid:
Title: 'Combined DESeq results'
...
bigwig:
type: File
format: "http://edamontology.org/format_3006"
label: "BigWig file"
doc: "Generated BigWig file"
outputSource: bam_to_bigwig/bigwig_file
'sd:visualPlugins':
- igvbrowser:
id: 'igvbrowser'
type: 'wig'
name: "BigWig Track"
height: 120
...The 'sd:serviceTag'keyword enables new workflows to be added for the creation of:
- samples: uses keyword
'sample' - analyses: uses keyword
'analysis' - genelist: uses keywork
'genelist'