Explore Workflows

Comvert BAM to BEDPE and compress the output

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/bamtobedpe-gzip.cwl

Branch/Commit ID: 265440c63ab75d2451c90bcd116e725626e9a608

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

https://github.com/datirium/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 46a077b51619c6a14f85e0aa5260ae8a04426fab

https://github.com/reanahub/reana-demo-helloworld.git

Path: workflow/cwl/helloworld-htcondorcern.cwl

Branch/Commit ID: cc0bff51d5e80662cbd2b687005bb0cdcf491a88

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf6.cwl

Branch/Commit ID: 9f3b9e7b74d5a904b12674dfd1300b56a48c3d33

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: 8c4e7372247a7f4ed9ed478ef8ea1d239bc88af0

https://github.com/reanahub/reana-demo-worldpopulation.git

Path: workflow/cwl/worldpopulation.cwl

Branch/Commit ID: 10b0887259e29e9e5b87dcc7e437d23fca549e39

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/sv_paired_read_caller_filter.cwl

Branch/Commit ID: 8c4e7372247a7f4ed9ed478ef8ea1d239bc88af0

Differential Binding Analysis of ChIP-Seq Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. For more information please refer to: ------------------------------------- Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S, Palmieri C, Caldas C, Carroll JS (2012). “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.” Nature, 481, -4.

https://github.com/datirium/workflows.git

Path: workflows/diffbind.cwl

Branch/Commit ID: 46a077b51619c6a14f85e0aa5260ae8a04426fab

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea