Workflow: ChIP-seq peak caller workflow MACS2 based
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/master/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 | 3121f1aaf58f2a12860597bd145b01cc[] | ||
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/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/ChIP-Seq/peak-calling-MACS2.cwl