Workflow: 04-peakcall.cwl

Fetched 2019-03-19 14:59:20 GMT

ChIP-seq 04 quantification - samples: treatment.

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Inputs

ID Type Title Doc
as_broadPeak_file File

Definition broadPeak file in AutoSql format (used in bedToBigBed)

as_narrowPeak_file File

Definition narrowPeak file in AutoSql format (used in bedToBigBed)

input_bam_files File[]
nthreads Integer
genome_effective_size String

Effective genome size used by MACS2. It can be numeric or a shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs

input_genome_sizes File

Two column tab-delimited file with chromosome size information

Steps

ID Runs Label Doc
narrowpeaks-bed-to-bigbed
../quant/bedToBigBed.cwl (CommandLineTool)

\"bedToBigBed v. 2.7 - Convert bed file to bigBed. (BigBed version: 4) usage: bedToBigBed in.bed chrom.sizes out.bb Where in.bed is in one of the ascii bed formats, but not including track lines and chrom.sizes is two column: <chromosome name> <size in bases> and out.bb is the output indexed big bed file. Use the script: fetchChromSizes to obtain the actual chrom.sizes information from UCSC, please do not make up a chrom sizes from your own information. The in.bed file must be sorted by chromosome,start, to sort a bed file, use the unix sort command: sort -k1,1 -k2,2n unsorted.bed > sorted.bed\"

extract-count-reads-in-narrowpeaks
../peak_calling/samtools-extract-number-mapped-reads.cwl (CommandLineTool)

Extract mapped reads from BAM file using Samtools flagstat command

trunk-broadpeak-score
../utils/trunk-peak-score.cwl (CommandLineTool)

Trunk scores in ENCODE bed6+4 files

count-narrowpeaks
../utils/count-with-output-suffix.cwl (CommandLineTool)

Counts lines in a file and returns a suffixed file with that number

filter-reads-in-narrowpeaks
../peak_calling/samtools-filter-in-bedfile.cwl (CommandLineTool)

Filter BAM file to only include reads overlapping with a BED file

count-reads-filtered
../peak_calling/count-reads-after-filtering.cwl (CommandLineTool)

Count number of dedup-ed reads used in peak calling

broadpeaks-bed-to-bigbed
../quant/bedToBigBed.cwl (CommandLineTool)

\"bedToBigBed v. 2.7 - Convert bed file to bigBed. (BigBed version: 4) usage: bedToBigBed in.bed chrom.sizes out.bb Where in.bed is in one of the ascii bed formats, but not including track lines and chrom.sizes is two column: <chromosome name> <size in bases> and out.bb is the output indexed big bed file. Use the script: fetchChromSizes to obtain the actual chrom.sizes information from UCSC, please do not make up a chrom sizes from your own information. The in.bed file must be sorted by chromosome,start, to sort a bed file, use the unix sort command: sort -k1,1 -k2,2n unsorted.bed > sorted.bed\"

narrowPeak-calling
../peak_calling/macs2-callpeak.cwl (CommandLineTool)
count-broadpeaks
../utils/count-with-output-suffix.cwl (CommandLineTool)

Counts lines in a file and returns a suffixed file with that number

trunk-narrowpeak-score
../utils/trunk-peak-score.cwl (CommandLineTool)

Trunk scores in ENCODE bed6+4 files

extract-count-reads-in-broadpeaks
../peak_calling/samtools-extract-number-mapped-reads.cwl (CommandLineTool)

Extract mapped reads from BAM file using Samtools flagstat command

filter-reads-in-broadpeaks
../peak_calling/samtools-filter-in-bedfile.cwl (CommandLineTool)

Filter BAM file to only include reads overlapping with a BED file

spp
../spp/spp.cwl (CommandLineTool)
broadPeak-calling
../peak_calling/macs2-callpeak.cwl (CommandLineTool)
extract-peak-frag-length
../spp/extract-best-frag-length.cwl (CommandLineTool)

Extracts best fragment length from SPP output text file

Outputs

ID Type Label Doc
output_broadpeak_count File[]

Peak counts within replicate

output_narrowpeak_xls_file File[]

Peak calling report file (*_peaks.xls file produced by MACS2)

output_narrowpeak_file File[]

peakshift/phantomPeak results file

output_broadpeak_xls_file File[]

Peak calling report file (*_peaks.xls file produced by MACS2)

output_broadpeak_file File[]

peakshift/phantomPeak results file

output_narrowpeak_summits_file 7ffceaadf9147dc285ac250d5b7f9829[]

File containing peak summits

output_broadpeak_summits_file ed7a1326417617a1187dc17b8b7ee44b[]

File containing peak summits

output_filtered_read_count_file File[]

Filtered read count reported by MACS2

output_read_in_narrowpeak_count_within_replicate File[]

narrowPeak counts within replicate

output_narrowpeak_bigbed_file File[]

Peaks in bigBed format

output_read_in_broadpeak_count_within_replicate File[]

broadPeak counts within replicate

output_spp_x_cross_corr File[]

peakshift/phantomPeak results file

output_spp_cross_corr_plot File[]

peakshift/phantomPeak results file

output_narrowpeak_count File[]

Peak counts within replicate

output_broadpeak_bigbed_file File[]

Peaks in bigBed format

Permalink: https://w3id.org/cwl/view/git/6d9457382f0b7cc2510e148d21383261280d17ed/v1.0/ChIP-seq_pipeline/04-peakcall.cwl