Workflow: ChIP-seq peak caller workflow MACS2 based
Fetched 2023-01-09 11:46:16 GMT
Verified with cwltool version 3.1.20221201130942
This workflow execute peak caller and QC for ChIP-seq using MACS2
- 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/11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| extsize | Integer (Optional) | ||
| nomodel | Boolean (Optional) | ||
| genome_gtf | File | ||
| genome_name | String | ||
| tagAlign_gz | File[] | ||
| genome_fasta | File | ||
| macs_callpeaks_g | String | ||
| macs_callpeaks_q | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| readQC |
../../tools/R/readQC.cwl
(CommandLineTool)
|
readQC |
NGS read Quality Control analysis |
| gzip_cat |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| homer_tags |
../../tools/homer/homer-makeTagDirectory.cwl
(CommandLineTool)
|
HOMER-makeTagDirectory |
Software for motif discovery and next generation sequencing analysis |
| macs_cutoff |
../../tools/R/macs-cutoff.cwl
(CommandLineTool)
|
MACS2_cutoff |
Inflection point calculated from MACS2 peaks file |
| macs_callpeak |
../../tools/macs/macs2-callpeak.cwl
(CommandLineTool)
|
MACS2-callpeak |
BASH echo command |
| lambda_bdg_to_tdf |
../../tools/igvtools/igvtools-totdf.cwl
(CommandLineTool)
|
igvtools-toTDF |
The igvtools utility provides a set of tools for pre-processing data files |
| pileup_bdg_to_tdf |
../../tools/igvtools/igvtools-totdf.cwl
(CommandLineTool)
|
igvtools-toTDF |
The igvtools utility provides a set of tools for pre-processing data files |
| homer_annotate_peaks |
../../tools/homer/homer-annotatePeaks.cwl
(CommandLineTool)
|
HOMER-annotatePeaks |
Software for motif discovery and next generation sequencing analysis |
| macs_callpeak_q_value |
../../tools/macs/macs2-callpeak.cwl
(CommandLineTool)
|
MACS2-callpeak |
BASH echo command |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| readQC_plots | 27dea07cfbfc5edad26ca03096afcad9[] | ||
| lambda_tdf_out | File[] | ||
| pileup_tdf_out | File[] | ||
| macs_cutoff_pdf | File[] | ||
| macs_cutoff_inflection | File[] | ||
| macs_callpeak_q_value_bed | File[] | ||
| macs_callpeak_q_value_xls | File[] | ||
| homer_annotate_peaks_output | File[] | ||
| homer_annotate_peaks_annStats | File[] (Optional) | ||
| macs_callpeak_q_value_narrowPeak | File[] |
Permalink:
https://w3id.org/cwl/view/git/11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419/workflows/ChIP-Seq/peak-calling-MACS2.cwl
