Workflow: wf_full_IDR_pipeline_2inputs_sample.cwl
Fetched 2024-05-18 21:53:05 GMT
Verified with cwltool version 3.1.20221201130942
This workflow essentially restructures the inputs before sending to wf_full_IDR_pipeline_2inputs.cwl
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| sample | c1ce4692bd14f84e5cd3d93f96d50b57[] | ||
| species | String | ||
| chrom_sizes | File | ||
| split_peaks_bed | String | ||
| split_peaks_custombed | String | ||
| rep1_merged_peaks_bed_from_cc | String | ||
| rep2_merged_peaks_bed_from_cc | String | ||
| rep1_merged_peaks_custombed_from_cc | String | ||
| rep2_merged_peaks_custombed_from_cc | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| step_parse_sample_IDR |
parse_sample_IDR.cwl
(ExpressionTool)
|
This expressiontool parses an IDR record sample object into distinct reads |
|
| wf_full_IDR_pipeline_2inputs |
wf_full_IDR_pipeline_2inputs.cwl
(Workflow)
|
The main workflow that: produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each). runs the 'rescue ratio' statistic runs the 'consistency ratio' statistic |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| idr_output | File | ||
| rescue_ratio | 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 | ||
| reproducible_peaks | File | ||
| rep1_compressed_bed | File | ||
| rep1_input_read_num | File | ||
| rep2_compressed_bed | File | ||
| rep2_input_read_num | File | ||
| rep1_input_normed_bed | File | ||
| rep2_input_normed_bed | File | ||
| rep1_input_normed_full | File | ||
| rep2_input_normed_full | File | ||
| self_consistency_ratio | File | ||
| rep1_entropy_excess_reads | File | ||
| rep2_entropy_excess_reads | File | ||
| reproducible_peaks_bigbed | File | ||
| rep1_reproducing_peaks_full | File | ||
| rep2_reproducing_peaks_full | File | ||
| reproducible_peaks_narrowpeak | 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/aedc0a14d4ba109ee65678a3201a52c5bb6ad473/cwl/wf_full_IDR_pipeline_2inputs_sample.cwl
