Workflow: ChIP-seq peak caller workflow MACS2 based

Fetched 2022-08-09 19:03:04 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)
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 46f291fd25eaa1ff680a5f458b3cccc0[]
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/2219466121978031f1f3bff91de74e82eb3f5640/workflows/ChIP-Seq/peak-calling-MACS2.cwl