CWL Workflow: wf_get_peaks_pe.cwl

Workflow: wf_get_peaks_pe.cwl

Fetched 2023-04-15 13:39:53 GMT

Verified with cwltool version 3.1.20230201224320

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This workflow is Open Source and may be reused according to the terms of: https://raw.githubusercontent.com/YeoLab/eclip/c0fffc4979a92371dc0667a03e3d957bf7f77600/LICENSE

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
sample	12d2b368a69f231fde596a1c576e2a4c[]
dataset	String
species	String
chrom_sizes	File
barcodesfasta	File
randomer_length	String
speciesGenomeDir	Directory
repeatElementGenomeDir	Directory

Steps

ID	Runs	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_index_ip	samtools-index.cwl (CommandLineTool)	samtools-index.cwl is developed for CWL consortium
step_index_input	samtools-index.cwl (CommandLineTool)	samtools-index.cwl is developed for CWL consortium
step_ip_alignment	wf_clipseqcore_pe_2barcodes.cwl (Workflow)	Workflow for handling reads containing two barcodes. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs
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	wf_clipseqcore_pe_1barcode.cwl (Workflow)	Workflow for handling reads containing one barcode. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs
step_calculate_entropy	calculate_entropy.cwl (CommandLineTool)	This tool computes and sums the entropy values for significant peaks (l10p >=3 and l2fc >=3). Returns the number as a file.
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:

Outputs

ID	Type	Label	Doc
output_input_bam	File
output_ip_neg_bw	File
output_ip_pos_bw	File
output_entropynum	File
output_clipper_bed	File
output_input_neg_bw	File
output_input_pos_bw	File
output_ip_merged_bam	File
output_compressed_peaks	File
output_inputnormed_peaks	File
output_ip_b1_trimx1_fastq	File[]
output_ip_b1_trimx2_fastq	File[]
output_ip_b2_trimx1_fastq	File[]
output_ip_b2_trimx2_fastq	File[]
output_ip_b1_trimx1_metrics	File
output_ip_b1_trimx2_metrics	File
output_ip_b2_trimx1_metrics	File
output_ip_b2_trimx2_metrics	File
output_input_b1_trimx1_fastq	File[]
output_input_b1_trimx2_fastq	File[]
output_ip_b1_mapgenome_stats	File
output_ip_b2_mapgenome_stats	File
output_ip_b1_demuxed_fastq_r1	File
output_ip_b1_demuxed_fastq_r2	File
output_ip_b1_maprepeats_stats	File
output_ip_b2_demuxed_fastq_r1	File
output_ip_b2_demuxed_fastq_r2	File
output_ip_b2_maprepeats_stats	File
output_input_b1_trimx1_metrics	File
output_input_b1_trimx2_metrics	File
output_ip_b1_output_sorted_bam	File
output_ip_b2_output_sorted_bam	File
output_input_b1_mapgenome_stats	File
output_input_b1_demuxed_fastq_r1	File
output_input_b1_demuxed_fastq_r2	File
output_input_b1_maprepeats_stats	File
output_ip_b1_prermdup_sorted_bam	File
output_ip_b2_prermdup_sorted_bam	File
output_input_b1_output_sorted_bam	File
output_ip_b1_barcodecollapsepe_bam	File
output_ip_b1_sorted_unmapped_fastq	File[]
output_ip_b2_barcodecollapsepe_bam	File
output_ip_b2_sorted_unmapped_fastq	File[]
output_input_b1_prermdup_sorted_bam	File
output_ip_b1_trimx1_fastqc_stats_R1	File
output_ip_b1_trimx1_fastqc_stats_R2	File
output_ip_b1_trimx2_fastqc_stats_R1	File
output_ip_b1_trimx2_fastqc_stats_R2	File
output_ip_b2_trimx1_fastqc_stats_R1	File
output_ip_b2_trimx1_fastqc_stats_R2	File
output_ip_b2_trimx2_fastqc_stats_R1	File
output_ip_b2_trimx2_fastqc_stats_R2	File
output_ip_b1_mapgenome_star_settings	File
output_ip_b1_trimx1_fastqc_report_R1	File
output_ip_b1_trimx1_fastqc_report_R2	File
output_ip_b1_trimx2_fastqc_report_R1	File
output_ip_b1_trimx2_fastqc_report_R2	File
output_ip_b2_mapgenome_star_settings	File
output_ip_b2_trimx1_fastqc_report_R1	File
output_ip_b2_trimx1_fastqc_report_R2	File
output_ip_b2_trimx2_fastqc_report_R1	File
output_ip_b2_trimx2_fastqc_report_R2	File
output_input_b1_barcodecollapsepe_bam	File
output_input_b1_sorted_unmapped_fastq	File[]
output_ip_b1_maprepeats_star_settings	File
output_ip_b2_maprepeats_star_settings	File
output_input_b1_trimx1_fastqc_stats_R1	File
output_input_b1_trimx1_fastqc_stats_R2	File
output_input_b1_trimx2_fastqc_stats_R1	File
output_input_b1_trimx2_fastqc_stats_R2	File
output_ip_b1_barcodecollapsepe_metrics	File
output_ip_b2_barcodecollapsepe_metrics	File
output_input_b1_mapgenome_star_settings	File
output_input_b1_trimx1_fastqc_report_R1	File
output_input_b1_trimx1_fastqc_report_R2	File
output_input_b1_trimx2_fastqc_report_R1	File
output_input_b1_trimx2_fastqc_report_R2	File
output_ip_b1_mapgenome_mapped_to_genome	File
output_ip_b2_mapgenome_mapped_to_genome	File
output_input_b1_maprepeats_star_settings	File
output_ip_b1_maprepeats_mapped_to_genome	File
output_ip_b2_maprepeats_mapped_to_genome	File
output_input_b1_barcodecollapsepe_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/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_get_peaks_pe.cwl