Workflow: wf_get_reproducible_eclip_peaks.cwl

Fetched 2022-01-20 13:15:44 GMT

The main workflow that produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each).

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Inputs

ID Type Title Doc
merged_peaks_custombed String
rep1_peaks_bed_file File
rep2_clip_bam_file File
chrom_sizes File
merged_peaks_bed String
rep1_clip_bam_file File
species String
rep2_peaks_bed_file File
rep1_input_bam_file File
rep2_input_bam_file File

Steps

ID Runs Label Doc
step_bed_to_bigbed
bed_to_bigbed.cwl (CommandLineTool)

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

rep2_input_norm_and_entropy

This workflow normalizes clip aligned reads against a size-matched input sample. Then, an entropy score is calculated for each peak found.

rep1_input_norm_using_idr_peaks
overlap_peakfi_with_bam.cwl (CommandLineTool)

This tool wraps overlap_peakfi_with_bam_PE.pl Usage:

get_reproducing_peaks
get_reproducing_peaks.cwl (CommandLineTool)
rep2_input_norm_using_idr_peaks
overlap_peakfi_with_bam.cwl (CommandLineTool)

This tool wraps overlap_peakfi_with_bam_PE.pl Usage:

create_bed_from_idr
parse_idr_peaks.cwl (CommandLineTool)

returns the

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)

idr
idr.cwl (CommandLineTool)
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.

reproducible_peaks_file_to_int
file2int.cwl (ExpressionTool)

Returns string expression based on file contents.

rep1_input_norm_and_entropy

This workflow normalizes clip aligned reads against a size-matched input sample. Then, an entropy score is calculated for each peak found.

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

count_reproducing_peaks
linescount.cwl (CommandLineTool)

Outputs

ID Type Label Doc
rep1_entropy_bed File

entropy file re-formatted as a bed file for input to IDR

output_narrowpeak File
rep1_compressed_bed File

input normalized and compressed clip over input for rep1

rep2_entropy_bed File
rep2_input_normed_bed File
rep1_input_read_num File
rep1_entropy_excess_reads File
merged_peaks_bed_file File
output_bigbed File
rep2_input_normed_full File
rep2_reproducing_peaks_full File
merged_peaks_custombed_file File
rep2_clip_read_num File
rep2_entropy_full File
rep2_input_read_num File
rep2_entropy_excess_reads File
rep2_idr_output_input_normed_full File
rep1_entropy_full File

input normalized clip over input for rep1 with entropy info

idr_output File
rep1_reproducing_peaks_full File
rep2_idr_output_input_normed_bed File
rep2_compressed_bed File
rep1_input_normed_bed File

input normalized clip over input for rep1

rep1_idr_output_input_normed_full File
rep1_idr_output_input_normed_bed File
rep1_clip_read_num File

file containing mapped reads from rep1 clip BAM

idr_output_bed File
rep1_input_normed_full File

input normalized clip over input for rep1 with read info

reproducing_peaks_count Integer
Permalink: https://w3id.org/cwl/view/git/aedc0a14d4ba109ee65678a3201a52c5bb6ad473/cwl/wf_get_reproducible_eclip_peaks.cwl