Explore Workflows

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: 9850a859de1f42d3d252c50e15701928856fe774

Perform taxonomic identification tasks on an input genome

https://github.com/ncbi/pgap.git

Path: taxcheck.cwl

Branch/Commit ID: 6ac47e5703d8c8cdac698de91143829b3911e9b2

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 449bc7e45bb02316d040f73838ef18359e770268

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/pipelines/gathered_downsample_and_recall.cwl

Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8

Motif Finding with HOMER with target and background regions from peaks --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-peak.cwl

Branch/Commit ID: 104059e07a2964673e21d371763e33c0afeb2d03

https://github.com/aplbrain/saber.git

Path: saber/i2g/examples/I2G_Seg_Workflow/workflowSegment.cwl

Branch/Commit ID: d370ce1afd6b25be764b35069262fa23bc8f9974

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

Path: tests/wf/wffail.cwl

Branch/Commit ID: eba80916b5cde8bdbd56c077c94240ddf796a27b

This workflow creates a subsample from a BAM file creating a tagAlign and pseudoreplicates

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

Path: workflows/File-formats/subample-pseudoreplicates.cwl

Branch/Commit ID: 265440c63ab75d2451c90bcd116e725626e9a608

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: pipeline.cwl

Branch/Commit ID: c502823c0b078737ef4533b1509e25d58cb3a78a

Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-bg.cwl

Branch/Commit ID: 9850a859de1f42d3d252c50e15701928856fe774