Workflow: ChIP-seq peak caller workflow MACS2 based

Fetched 2022-01-20 13:12:08 GMT

This workflow execute peak caller and QC for ChIP-seq using MACS2

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Inputs

ID Type Title Doc
extsize Integer (Optional)
tagAlign_gz File[]
nomodel Boolean (Optional)
genome_name String
genome_fasta File
macs_callpeaks_q Float
macs_callpeaks_g String
genome_gtf File

Steps

ID Runs Label Doc
macs_cutoff
../../tools/R/macs-cutoff.cwl (CommandLineTool)
MACS2_cutoff

Inflection point calculated from MACS2 peaks file

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

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_callpeak
../../tools/macs/macs2-callpeak.cwl (CommandLineTool)
MACS2-callpeak

BASH echo command

macs_callpeak_q_value
../../tools/macs/macs2-callpeak.cwl (CommandLineTool)
MACS2-callpeak

BASH echo command

readQC
../../tools/R/readQC.cwl (CommandLineTool)
readQC

NGS read Quality Control analysis

homer_annotate_peaks
../../tools/homer/homer-annotatePeaks.cwl (CommandLineTool)
HOMER-annotatePeaks

Software for motif discovery and next generation sequencing analysis

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

Outputs

ID Type Label Doc
homer_annotate_peaks_annStats File[] (Optional)
macs_cutoff_inflection File[]
homer_annotate_peaks_output File[]
readQC_plots 5492cfec059364e3c29c7d6309a50ae0[]
macs_cutoff_pdf File[]
macs_callpeak_q_value_narrowPeak File[]
pileup_tdf_out File[]
lambda_tdf_out File[]
macs_callpeak_q_value_bed File[]
macs_callpeak_q_value_xls File[]
Permalink: https://w3id.org/cwl/view/git/11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419/workflows/ChIP-Seq/peak-calling-MACS2.cwl