Workflow: wf_full_IDR_pipeline_1input.cwl
Fetched 2023-01-03 22:04:05 GMT
Verified with cwltool version 3.1.20221201130942
The main workflow that: produces two reproducible peaks via IDR given two eCLIP samples (1 input total for both reps, 1 IP each replicate). runs the 'rescue ratio' statistic runs the 'consistency ratio' statistic
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Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| species | String | ||
| rep1_name | String | ||
| rep2_name | String | ||
| chrom_sizes | File | ||
| input_bam_file | File | ||
| split_peaks_bed | String | ||
| merged_peaks_bed | String | ||
| rep1_clip_bam_file | File | ||
| rep2_clip_bam_file | File | ||
| rep1_peaks_bed_file | File | ||
| rep2_peaks_bed_file | File | ||
| split_peaks_custombed | String | ||
| merged_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 |
|---|---|---|---|
| wf_rescue_ratio_1input |
wf_rescue_ratio_1input.cwl
(Workflow)
|
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. |
|
| wf_self_consistency_ratio |
wf_self_consistency_ratio.cwl
(Workflow)
|
Computes the self-consistency ratio (see Gabe's protocols paper, or CHIP SEQ). Given two replicates, split each and perform IDR on each fragment. Returns the ratio of max(N1, N2)/min(N1, N2) where N1, N2 are the numbers of reproducible peaks found between each rep split pair. |
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 |
https://w3id.org/cwl/view/git/aedc0a14d4ba109ee65678a3201a52c5bb6ad473/cwl/wf_full_IDR_pipeline_1input.cwl
