Workflow: wf_get_peaks_pe.cwl

Fetched 2023-01-04 10:51:57 GMT
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Inputs

ID Type Title Doc
sample 14c4606908f1c20ae6175e1838dcdbd1[]
dataset String
species String
chrom_sizes File
barcodesfasta File
randomer_length String
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_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

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

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_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_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
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