Workflow: chipseq_tf.cwl
Fetched 2025-11-04 20:18:26 GMT
Verified with cwltool version 3.1.20221201130942
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- |
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| idxbase | File |
Base filename of bwa index to map against |
|
| blacklist | File |
Blacklist regions to remove |
|
| replicates | ad0d78a35b6eb4868ebe6275138952fa[] |
List of replicates |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| idr |
tools/idr.cwl
(CommandLineTool)
|
||
| name_outputs |
chipseq_tf.cwl#name_outputs/b2411f9b-ce8d-4b10-8313-96ec82cabdbb
(ExpressionTool)
|
||
| align_control |
chipseq_tf_align.cwl
(Workflow)
|
||
| align_treatment |
chipseq_tf_align.cwl
(Workflow)
|
||
| pooled_call_peaks |
tools/macs-callpeak.cwl
(CommandLineTool)
|
||
| replicate_call_peaks |
tools/macs-callpeak.cwl
(CommandLineTool)
|
||
| pooled_replicates_control |
tools/samtools-merge.cwl
(CommandLineTool)
|
||
| pooled_replicates_treatment |
tools/samtools-merge.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| idr_narrowpeak_file | File |
Peaks surviving IDR using pooled peaks as oracle |
|
| pooled_narrowpeak_file | File |
Peaks for each replicate |
|
| replicate_narrowpeak_files | File[] |
Peaks from pooling replicates |
Permalink:
https://w3id.org/cwl/view/git/f6346c109000c92ae53183df844eece0ad63eeb7/chipseq_tf.cwl
