Workflow: abc-enhancer-gene-prediction
Fetched 2025-05-03 03:56:21 GMT
Verified with cwltool version 3.1.20230201224320
## Activity by Contact Model of Enhancer-Gene Specificity in Common Workflow Language [broadinstitute/ABC-Enhancer-Gene-Prediction: Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)](https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction)
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source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File | ||
| dhs | File |
wgEncodeUwDnaseK562AlnRep1.chr22.bam |
|
| genes | File | ||
| H3K27ac | File |
ENCFF384ZZM.chr22.bam |
|
| cell_type | String | ||
| sort_order | File | ||
| chrom_sizes | File |
example_chr22/reference/chr22 |
|
| hi_c_directory | Directory |
example_chr22/input_data/HiC/raw/ |
|
| hi_c_resolution | Integer | ||
| expression_table | File |
K562.ENCFF934YBO.TPM.txt |
|
| regions_blocklist | File | ||
| regions_includelist | File | ||
| ubiquitously_expressed_genes | File |
UbiquitouslyExpressedGenesHG19.txt |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| abc_step01 | abc_step01 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| abc_step01_outputs | File[] | ABC Step01 Outputs | |
| run_neighborhood_output | File[] | Run Neighborhoods Output |
Candidate enhancer regions with Dnase-seq and H3K27ac ChIP-seq read counts |
| outputs_compute_abc_score | File[] |
Permalink:
https://w3id.org/cwl/view/git/6146d0867e60b9f72da3239fd800bfc5dc914700/abc_enhancer_gene_prediction/abc-enchancer-gene-prediction-wf.cwl
