Workflow: MACE ChIP-exo peak caller workflow for single-end samples
Fetched 2023-01-11 20:12:16 GMT
Verified with cwltool version 3.1.20221201130942
This workflow execute peak caller and QC from ChIP-exo for single-end samples using MACE
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/8967e816cb89dd9349c8c6deff686aeb8b118f1c/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| tss_size | Integer | ||
| chrom_size | File | ||
| genome_gtf | File | ||
| sorted_bam | b64f535fe270bb51e71eac83b185a1d4[] | ||
| norm_method | String | ||
| output_basename | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| mace |
../../tools/mace/mace.cwl
(CommandLineTool)
|
MACE |
Model based Analysis of ChIP Exo |
| bamscale_cov |
../../tools/bamscale/bamscale-cov.cwl
(CommandLineTool)
|
BAMscale-cov |
Calculate coverage of BED coordinates in BAM file(s) |
| preprocessor |
../../tools/mace/preprocessor.cwl
(CommandLineTool)
|
MACE-preprocessor |
Model based Analysis of ChIP Exo |
| annotate_bed_gff |
../../tools/python/annotate_bed_gtf.cwl
(CommandLineTool)
|
annotate_bed |
This tools annotate bed files from GFF |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| annotated_bed | File[] |
Permalink:
https://w3id.org/cwl/view/git/8967e816cb89dd9349c8c6deff686aeb8b118f1c/workflows/ChIP-exo/peak-caller-MACE-SE.cwl
