Explore Workflows

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Graph Name Retrieved From View
workflow graph heatmap.cwl

Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

https://github.com/Barski-lab/workflows.git

Path: workflows/heatmap.cwl

Branch/Commit ID: e89b2c17aa5efccef6ca424dec5a0a021bd8d20c
workflow graph heatmap-prepare.cwl

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

https://github.com/Barski-lab/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: e89b2c17aa5efccef6ca424dec5a0a021bd8d20c
workflow graph heatmap-prepare.cwl

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

https://github.com/barski-lab/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: e89b2c17aa5efccef6ca424dec5a0a021bd8d20c
workflow graph chipseq-pe.cwl

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

https://github.com/Barski-lab/workflows.git

Path: workflows/chipseq-pe.cwl

Branch/Commit ID: 12edfc2207507e53c6b5bb21e50decb5535a12f7
workflow graph Single-cell RNA-Seq Alignment

Single-cell RNA-Seq Alignment Runs Cell Ranger Count to quantify gene expression from a single-cell RNA-Seq library.

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-rna-align-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731
workflow graph Single-cell Multiome ATAC and RNA-Seq Aggregate

Single-cell Multiome ATAC and RNA-Seq Aggregate Aggregates data from multiple Single-cell Multiome ATAC and RNA-Seq Alignment experiments

 https://github.com/Barski-lab/sc-seq-analysis.git

Path: workflows/sc-multiome-aggregate-wf.cwl

Branch/Commit ID: e70b7fab45e4bd2abfb7dab2b8b1f79ce904ac69
workflow graph Single-cell Multiome ATAC and RNA-Seq Alignment

Single-cell Multiome ATAC and RNA-Seq Alignment Runs Cell Ranger ARC Count to quantifies chromatin accessibility and gene expression from a single-cell Multiome ATAC and RNA-Seq library

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-multiome-align-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731
workflow graph Single-cell RNA-Seq Aggregate

Single-cell RNA-Seq Aggregate Aggregates gene expression data from multiple Single-cell RNA-Seq Alignment experiments.

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-rna-aggregate-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731
workflow graph Single-cell Multiome ATAC and RNA-Seq Aggregate

Single-cell Multiome ATAC and RNA-Seq Aggregate Aggregates data from multiple Single-cell Multiome ATAC and RNA-Seq Alignment experiments

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-multiome-aggregate-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731
workflow graph Single-cell Reference Indices

Single-cell Reference Indices Builds a Cell Ranger and Cell Ranger ARC compatible reference folders from the custom genome FASTA and gene GTF annotation files

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-ref-indices-wf.cwl

Branch/Commit ID: 7bbe737324bb6f21f244dea09a926dc2774ed731