Workflow: wf_get_reproducible_eclip_peaks.cwl
Fetched 2023-01-12 06:57:50 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
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| 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)
|
||
| create_bed_from_idr |
parse_idr_peaks.cwl
(CommandLineTool)
|
returns the |
|
| get_reproducing_peaks |
get_reproducing_peaks.cwl
(CommandLineTool)
|
||
| 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 Usage: |
|
| rep2_input_norm_using_idr_peaks |
overlap_peakfi_with_bam.cwl
(CommandLineTool)
|
This tool wraps Usage: |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| idr_output | File | ||
| idr_output_bed | File | ||
| rep1_entropy_bed | File | ||
| rep2_entropy_bed | File | ||
| rep1_entropy_full | File | ||
| rep2_entropy_full | File | ||
| rep1_clip_read_num | File | ||
| rep2_clip_read_num | File | ||
| rep1_input_read_num | File | ||
| rep2_input_read_num | File | ||
| merged_peaks_bed_file | File | ||
| rep1_input_normed_bed | File | ||
| rep2_input_normed_bed | File | ||
| rep1_input_normed_full | File | ||
| 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 |
Permalink:
https://w3id.org/cwl/view/git/b922446e59a5e8afbc75e88d09567e256cefbbfd/cwl/wf_get_reproducible_eclip_peaks.cwl
