Workflow: 04-peakcall-pe.cwl
Fetched 2024-11-14 12:28:40 GMT
Verified with cwltool version 3.1.20221201130942
ATAC-seq 04 quantification - PE
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer | ||
| input_bam_files | File[] | ||
| as_narrowPeak_file | File |
Definition narrowPeak file in AutoSql format (used in bedToBigBed) |
|
| input_genome_sizes | File |
Two column tab-delimited file with chromosome size information |
|
| 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 |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| spp |
../spp/spp.cwl
(CommandLineTool)
|
||
| count-peaks |
../utils/count-with-output-suffix.cwl
(CommandLineTool)
|
Counts lines in a file and returns a suffixed file with that number |
|
| peak-calling |
../peak_calling/macs2-callpeak.cwl
(CommandLineTool)
|
||
| unpair_bedpe |
../peak_calling/bedpe-to-bed.cwl
(CommandLineTool)
|
Un-pack a BEDPE concatenating both mates so that they are treated independently |
|
| clip-off-chrom |
../quant/bedClip.cwl
(CommandLineTool)
|
\"Tool: bedClip - Remove lines from bed file that refer to off-chromosome places. usage: bedClip input.bed chrom.sizes output.bed chrom.sizes is a two-column file/URL: <chromosome name> <size in bases> If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like http://hgdownload.cse.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes or you may use the script fetchChromSizes to download the chrom.sizes file. If not hosted by UCSC, a chrom.sizes file can be generated by running twoBitInfo on the assembly .2bit file. options: -verbose=2 - set to get list of lines clipped and why\" |
|
| 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 |
|
| bedtools_bamtobed |
../map/bedtools-bamtobed.cwl
(CommandLineTool)
|
||
| 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\" |
|
| count-peaks-unpaired |
../utils/count-with-output-suffix.cwl
(CommandLineTool)
|
Counts lines in a file and returns a suffixed file with that number |
|
| count-reads-filtered |
../peak_calling/count-reads-after-filtering.cwl
(CommandLineTool)
|
Count number of dedup-ed reads used in peak calling |
|
| filter-reads-in-peaks |
../peak_calling/samtools-filter-in-bedfile.cwl
(CommandLineTool)
|
Filter BAM file to only include reads overlapping with a BED file |
|
| peak-calling-unpaired |
../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 |
|
| trunk-peak-score-unpaired |
../utils/trunk-peak-score.cwl
(CommandLineTool)
|
Trunk scores in ENCODE bed6+4 files |
|
| extract-count-reads-in-peaks |
../peak_calling/samtools-extract-number-mapped-reads.cwl
(CommandLineTool)
|
Extract mapped reads from BAM file using Samtools flagstat command |
|
| 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\" |
|
| count-reads-filtered-unpaired |
../peak_calling/count-reads-after-filtering.cwl
(CommandLineTool)
|
Count number of dedup-ed reads used in peak calling |
|
| 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 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_peak_file | File[] |
peakshift/phantomPeak results file |
|
| output_peak_xls_file | File[] |
Peak calling report file (*_peaks.xls file produced by MACS2) |
|
| output_peak_bigbed_file | File[] |
Peaks in bigBed format |
|
| output_spp_x_cross_corr | File[] |
peakshift/phantomPeak results file |
|
| output_peak_summits_file | File[] |
File containing peak summits |
|
| output_extended_peak_file | File[] |
peakshift/phantomPeak extended fragment results file |
|
| output_unpaired_peak_file | File[] |
peakshift/phantomPeak results file using each paired mate independently |
|
| output_spp_cross_corr_plot | File[] |
peakshift/phantomPeak results file |
|
| output_unpaired_peak_xls_file | File[] |
Peak calling report file (*_peaks.xls file produced by MACS2) using each paired mate independently |
|
| output_filtered_read_count_file | File[] |
Filtered read count reported by MACS2 |
|
| output_unpaired_peak_bigbed_file | File[] |
Peaks in bigBed format using each paired mate independently |
|
| output_unpaired_peak_summits_file | File[] |
File containing peak summits using each paired mate independently |
|
| output_peak_count_within_replicate | File[] |
Peak counts within replicate |
|
| output_unpaired_extended_peak_file | File[] |
peakshift/phantomPeak extended fragment results file using each paired mate independently |
|
| output_unpaired_filtered_read_count_file | File[] |
Filtered read count reported by MACS2 using each paired mate independently |
|
| output_read_in_peak_count_within_replicate | File[] |
Reads peak counts within replicate |
|
| output_unpaired_peak_count_within_replicate | File[] |
Peak counts within replicate using each paired mate independently |
https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl
