Workflow: 04-peakcall-pe.cwl

Fetched 2019-06-27 12:11:18 GMT

ATAC-seq 04 quantification - PE

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Inputs

ID Type Title Doc
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
trunk-peak-score-unpaired
../utils/trunk-peak-score.cwl (CommandLineTool)

Trunk scores in ENCODE bed6+4 files

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

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

peaks-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\"

peak-calling-unpaired
../peak_calling/macs2-callpeak.cwl (CommandLineTool)
filter-reads-in-peaks-unpaired
../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

peaks-bed-to-bigbed-unpaired
../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-peaks
../peak_calling/samtools-extract-number-mapped-reads.cwl (CommandLineTool)

Extract mapped reads from BAM file using Samtools flagstat command

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

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

spp
../spp/spp.cwl (CommandLineTool)
extract-peak-frag-length
../spp/extract-best-frag-length.cwl (CommandLineTool)

Extracts best fragment length from SPP output text file

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

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

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

Count number of dedup-ed reads used in peak calling

sort-bam-by-name
../map/samtools-sort.cwl (CommandLineTool)
trunk-peak-score
../utils/trunk-peak-score.cwl (CommandLineTool)

Trunk scores in ENCODE bed6+4 files

unpair_bedpe
../peak_calling/bedpe-to-bed.cwl (CommandLineTool)

Un-pack a BEDPE concatenating both mates so that they are treated independently

bedtools_bamtobed
../map/bedtools-bamtobed.cwl (CommandLineTool)
peak-calling
../peak_calling/macs2-callpeak.cwl (CommandLineTool)

Outputs

ID Type Label Doc
output_read_in_peak_count_within_replicate File[]

Reads peak counts within replicate

output_peak_count_within_replicate File[]

Peak counts within replicate

output_unpaired_peak_xls_file File[]

Peak calling report file (*_peaks.xls file produced by MACS2) using each paired mate independently

output_peak_xls_file File[]

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

output_filtered_read_count_file File[]

Filtered read count reported by MACS2

output_unpaired_peak_summits_file File[]

File containing peak summits using each paired mate independently

output_extended_peak_file File[]

peakshift/phantomPeak extended fragment results file

output_unpaired_peak_count_within_replicate File[]

Peak counts within replicate using each paired mate independently

output_peak_file File[]

peakshift/phantomPeak results file

output_unpaired_peak_bigbed_file File[]

Peaks in bigBed format using each paired mate independently

output_unpaired_peak_file File[]

peakshift/phantomPeak results file using each paired mate independently

output_peak_summits_file File[]

File containing peak summits

output_spp_x_cross_corr File[]

peakshift/phantomPeak results file

output_spp_cross_corr_plot File[]

peakshift/phantomPeak results file

output_unpaired_filtered_read_count_file File[]

Filtered read count reported by MACS2 using each paired mate independently

output_unpaired_extended_peak_file File[]

peakshift/phantomPeak extended fragment results file using each paired mate independently

output_peak_bigbed_file File[]

Peaks in bigBed format

Permalink: https://w3id.org/cwl/view/git/c269cecf317c699d6f3a0f44782e90914bce62b5/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl