Workflow: wf_get_reproducible_eclip_peaks.cwl
Fetched 2025-11-08 13:01:04 GMT
Verified with cwltool version 3.1.20221201130942
The main workflow that produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each).
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| species | String | ||
| chrom_sizes | File | ||
| merged_peaks_bed | String | ||
| rep1_clip_bam_file | File | ||
| rep2_clip_bam_file | File | ||
| rep1_input_bam_file | File | ||
| rep1_peaks_bed_file | File | ||
| rep2_input_bam_file | File | ||
| rep2_peaks_bed_file | File | ||
| merged_peaks_custombed | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| idr |
idr.cwl
(CommandLineTool)
|
||
| step_sort_bed |
sort-bed.cwl
(CommandLineTool)
|
This tool wraps unix sort to sort a BED file. |
|
| step_bed_to_bigbed |
bed_to_bigbed.cwl
(CommandLineTool)
|
This tool converts an input-normalized eCLIP peaks file (BED6) into a bigbed (bb) file. |
|
| create_bed_from_idr |
parse_idr_peaks.cwl
(CommandLineTool)
|
returns the |
|
| get_reproducing_peaks |
get_reproducing_peaks.cwl
(CommandLineTool)
|
||
| 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) |
|
| count_reproducing_peaks |
linescount.cwl
(CommandLineTool)
|
||
| rep1_input_norm_and_entropy |
wf_input_norm_and_entropy.cwl
(Workflow)
|
This workflow normalizes clip aligned reads against a size-matched input sample. Then, an entropy score is calculated for each peak found. |
|
| rep2_input_norm_and_entropy |
wf_input_norm_and_entropy.cwl
(Workflow)
|
This workflow normalizes clip aligned reads against a size-matched input sample. Then, an entropy score is calculated for each peak found. |
|
| reproducible_peaks_file_to_int |
file2int.cwl
(ExpressionTool)
|
Returns string expression based on file contents. |
|
| rep1_input_norm_using_idr_peaks |
overlap_peakfi_with_bam.cwl
(CommandLineTool)
|
This tool wraps overlap_peakfi_with_bam_PE.pl Usage: |
|
| rep2_input_norm_using_idr_peaks |
overlap_peakfi_with_bam.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 |
|---|---|---|---|
| idr_output | File | ||
| output_bigbed | File | ||
| idr_output_bed | File | ||
| rep1_entropy_bed | File |
entropy file re-formatted as a bed file for input to IDR |
|
| rep2_entropy_bed | File | ||
| output_narrowpeak | File | ||
| rep1_entropy_full | File |
input normalized clip over input for rep1 with entropy info |
|
| rep2_entropy_full | File | ||
| rep1_clip_read_num | File |
file containing mapped reads from rep1 clip BAM |
|
| rep2_clip_read_num | File | ||
| rep1_compressed_bed | File |
input normalized and compressed clip over input for rep1 |
|
| rep1_input_read_num | File | ||
| rep2_compressed_bed | File | ||
| rep2_input_read_num | File | ||
| merged_peaks_bed_file | File | ||
| rep1_input_normed_bed | File |
input normalized clip over input for rep1 |
|
| rep2_input_normed_bed | File | ||
| rep1_input_normed_full | File |
input normalized clip over input for rep1 with read info |
|
| rep2_input_normed_full | File | ||
| reproducing_peaks_count | Integer | ||
| rep1_entropy_excess_reads | File | ||
| rep2_entropy_excess_reads | File | ||
| merged_peaks_custombed_file | File | ||
| rep1_reproducing_peaks_full | File | ||
| rep2_reproducing_peaks_full | File | ||
| rep1_idr_output_input_normed_bed | File | ||
| rep2_idr_output_input_normed_bed | File | ||
| rep1_idr_output_input_normed_full | File | ||
| rep2_idr_output_input_normed_full | File |
https://w3id.org/cwl/view/git/aedc0a14d4ba109ee65678a3201a52c5bb6ad473/cwl/wf_get_reproducible_eclip_peaks.cwl
