Workflow: wf_rescue_ratio_2inputs.cwl
Fetched 2023-01-10 04:59:56 GMT
Verified with cwltool version 3.1.20221201130942
Calculates the rescue ratio (see Gabe's protocols paper), given two eCLIP IP samples and 2 size-matched input samples. Also returns the reproducible peaks given these two samples. This is different from the 1input workflow in that each INPUT is first merged together and is used downstream instead of the 1input version, which remains unmodified. Merged inputs are NOT used in calculating true reproducible peaks.
- Selected
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| species | String | ||
| rep1_name | String | ||
| rep2_name | String | ||
| chrom_sizes | File | ||
| split_peaks_bed | String | ||
| 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 | ||
| split_peaks_custombed | String | ||
| merged_peaks_custombed | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| step_rescue_ratio |
max_over_min.cwl
(CommandLineTool)
|
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| step_merge_clip_bams |
bams_merge.cwl
(CommandLineTool)
|
merges 2 bam files together |
|
| step_merge_input_bams |
bams_merge.cwl
(CommandLineTool)
|
merges 2 bam files together |
|
| step_split_merged_bam_and_idr |
wf_split_self_and_idr.cwl
(Workflow)
|
This workflow returns the reproducible number of split peaks given a single bam file and its size-matched input pair. This workflow splits the bam file first, but does not do anything to the input. |
|
| step_get_true_reproducing_peaks |
wf_get_reproducible_eclip_peaks.cwl
(Workflow)
|
The main workflow that produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each). |
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 | ||
| 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 |
https://w3id.org/cwl/view/git/aedc0a14d4ba109ee65678a3201a52c5bb6ad473/cwl/wf_rescue_ratio_2inputs.cwl
