Workflow: wf_get_peaks_se.cwl

Fetched 2023-01-05 07:09:01 GMT
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Inputs

ID Type Title Doc
sample 5d4a7ad83e5c61e49d1a9e44c4c6a9f2[]
dataset String
species String
chrom_sizes File
blacklist_file File
speciesGenomeDir Directory
repeatElementGenomeDir Directory

Steps

ID Runs Label Doc
step_clipper
clipper.cwl (CommandLineTool)

CLIPper is a tool to define peaks in your CLIP-seq dataset. CLIPper was developed in the Yeo Lab at the University of California, San Diego. Usage: clipper --bam CLIP-seq_reads.srt.bam --species hg19 --outfile CLIP-seq_reads.srt.peaks.bed

step_sort_bed
sort-bed.cwl (CommandLineTool)

This tool wraps unix sort to sort a BED file.

Usage: sort -k1,1 -k2,2n unsorted.bed > sorted.bed

step_ip_alignment
step_bed_to_bigbed
bed_to_bigbed.cwl (CommandLineTool)

This tool converts an input-normalized eCLIP peaks file (BED6) into a bigbed (bb) file.

step_compress_peaks
peakscompress.cwl (CommandLineTool)

This tool wraps compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, which merges neighboring or overlapping regions in a BED file. Usage: perl compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl <in.bed> <out.compressed.bed>

step_input_alignment
step_blacklist_remove
blacklist-remove.cwl (CommandLineTool)

Given a list of 'blacklist' regions, remove those regions from an input BED file This tool wraps bedtools intersect -v to remove blacklist regions

step_bed_to_narrowpeak
bed_to_narrowpeak.cwl (CommandLineTool)

This tool converts an input-normalized eCLIP peaks file (BED6) into a narrowPeak format for encode DCC. cols 9 and 10 are just blank, col 5 is 1000 for things that meet the >=3 l2fc and l10pval cutoffs and 200 otherwise (it’s just for ucsc track coloring)

step_ip_mapped_readnum
samtools-mappedreadnum.cwl (CommandLineTool)

samtools-view.cwl is developed for CWL consortium Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]

Options: -b output BAM -C output CRAM (requires -T) -1 use fast BAM compression (implies -b) -u uncompressed BAM output (implies -b) -h include header in SAM output -H print SAM header only (no alignments) -c print only the count of matching records -o FILE output file name [stdout] -U FILE output reads not selected by filters to FILE [null] -t FILE FILE listing reference names and lengths (see long help) [null] -T FILE reference sequence FASTA FILE [null] -L FILE only include reads overlapping this BED FILE [null] -r STR only include reads in read group STR [null] -R FILE only include reads with read group listed in FILE [null] -q INT only include reads with mapping quality >= INT [0] -l STR only include reads in library STR [null] -m INT only include reads with number of CIGAR operations consuming query sequence >= INT [0] -f INT only include reads with all bits set in INT set in FLAG [0] -F INT only include reads with none of the bits set in INT set in FLAG [0] -x STR read tag to strip (repeatable) [null] -B collapse the backward CIGAR operation -s FLOAT integer part sets seed of random number generator [0]; rest sets fraction of templates to subsample [no subsampling] -@ INT number of BAM compression threads [0]

step_input_mapped_readnum
samtools-mappedreadnum.cwl (CommandLineTool)

samtools-view.cwl is developed for CWL consortium Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]

Options: -b output BAM -C output CRAM (requires -T) -1 use fast BAM compression (implies -b) -u uncompressed BAM output (implies -b) -h include header in SAM output -H print SAM header only (no alignments) -c print only the count of matching records -o FILE output file name [stdout] -U FILE output reads not selected by filters to FILE [null] -t FILE FILE listing reference names and lengths (see long help) [null] -T FILE reference sequence FASTA FILE [null] -L FILE only include reads overlapping this BED FILE [null] -r STR only include reads in read group STR [null] -R FILE only include reads with read group listed in FILE [null] -q INT only include reads with mapping quality >= INT [0] -l STR only include reads in library STR [null] -m INT only include reads with number of CIGAR operations consuming query sequence >= INT [0] -f INT only include reads with all bits set in INT set in FLAG [0] -F INT only include reads with none of the bits set in INT set in FLAG [0] -x STR read tag to strip (repeatable) [null] -B collapse the backward CIGAR operation -s FLOAT integer part sets seed of random number generator [0]; rest sets fraction of templates to subsample [no subsampling] -@ INT number of BAM compression threads [0]

step_input_normalize_peaks
overlap_peakfi_with_bam_PE.cwl (CommandLineTool)

This tool wraps overlap_peakfi_with_bam_PE.pl Usage:

step_fix_bed_for_bigbed_conversion
fix_bed_for_bigbed_conversion.cwl (CommandLineTool)

This tool fixes the eCLIP input-normalized format to the proper BED6 format prior to bigbed conversion.

Outputs

ID Type Label Doc
output_bigbed File
output_fixed_bed File
output_ip_neg_bw File
output_ip_pos_bw File
output_narrowpeak File
output_clipper_bed File
output_input_neg_bw File
output_input_pos_bw File
output_compressed_peaks File
output_inputnormed_peaks File
output_ip_b1_trimx1_fastq File[]
output_ip_b1_trimx2_fastq File[]
output_ip_b1_trimx1_metrics File
output_ip_b1_trimx2_metrics File
output_blacklist_removed_bed File
output_input_b1_trimx1_fastq File[]
output_input_b1_trimx2_fastq File[]
output_ip_b1_mapgenome_stats File
output_ip_b1_demuxed_fastq_r1 File
output_ip_b1_maprepeats_stats File
output_ip_b1_rmdup_sorted_bam File
output_input_b1_trimx1_metrics File
output_input_b1_trimx2_metrics File
output_input_b1_mapgenome_stats File
output_input_b1_demuxed_fastq_r1 File
output_input_b1_maprepeats_stats File
output_input_b1_rmdup_sorted_bam File
output_ip_b1_trimx1_fastqc_stats File
output_ip_b1_trimx2_fastqc_stats File
output_ip_b1_pre_rmdup_sorted_bam File
output_ip_b1_trimx1_fastqc_report File
output_ip_b1_trimx2_fastqc_report File
output_ip_b1_sorted_unmapped_fastq File
output_input_b1_trimx1_fastqc_stats File
output_input_b1_trimx2_fastqc_stats File
output_input_b1_pre_rmdup_sorted_bam File
output_input_b1_trimx1_fastqc_report File
output_input_b1_trimx2_fastqc_report File
output_ip_b1_mapgenome_star_settings File
output_input_b1_sorted_unmapped_fastq File
output_ip_b1_maprepeats_star_settings File
output_ip_b1_barcodecollapsese_metrics File
output_input_b1_mapgenome_star_settings File
output_ip_b1_mapgenome_mapped_to_genome File
output_input_b1_maprepeats_star_settings File
output_ip_b1_maprepeats_mapped_to_genome File
output_input_b1_barcodecollapsese_metrics File
output_input_b1_mapgenome_mapped_to_genome File
output_input_b1_maprepeats_mapped_to_genome File
Permalink: https://w3id.org/cwl/view/git/6b533898c395e9e5b9d0acc1587d0c68bc56abe0/cwl/wf_get_peaks_se.cwl