Workflow: Chipseq alignment with qc and creating homer tag directory
Fetched 2025-10-21 02:26:21 GMT
Verified with cwltool version 3.1.20230201224320
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| mills | File | ||
| omni_vcf | File | ||
| dbsnp_vcf | File | ||
| intervals | File | ||
| reference | File | ||
| final_name | String (Optional) | ||
| known_indels | File | ||
| bqsr_intervals | String[] | ||
| chipseq_sequence | https://w3id.org/cwl/view/git/3a822294da63b4e19446a285e2fef075e23cf3d0/definitions/types/sequence_data.yml#sequence_data[] | ||
| summary_intervals | https://w3id.org/cwl/view/git/3a822294da63b4e19446a285e2fef075e23cf3d0/definitions/types/labelled_file.yml#labelled_file[] (Optional) | ||
| per_base_intervals | https://w3id.org/cwl/view/git/3a822294da63b4e19446a285e2fef075e23cf3d0/definitions/types/labelled_file.yml#labelled_file[] (Optional) | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/3a822294da63b4e19446a285e2fef075e23cf3d0/definitions/types/labelled_file.yml#labelled_file[] (Optional) | ||
| minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc |
../subworkflows/qc_wgs.cwl
(Workflow)
|
WGS QC workflow | |
| alignment |
../subworkflows/sequence_to_bqsr.cwl
(Workflow)
|
Raw sequence data to BQSR | |
| bam_to_sam |
../tools/bam_to_sam.cwl
(CommandLineTool)
|
BAM to SAM conversion | |
| homer_tag_directory |
../tools/homer_tag_directory.cwl
(CommandLineTool)
|
Creating the homer tag directory |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| flagstats | File | ||
| wgs_metrics | File | ||
| tag_directory | Directory | ||
| gc_bias_metrics | File | ||
| summary_hs_metrics | File[] | ||
| insert_size_metrics | File | ||
| per_base_hs_metrics | File[] | ||
| verify_bam_id_depth | File | ||
| gc_bias_metrics_chart | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File[] | ||
| verify_bam_id_metrics | File | ||
| gc_bias_metrics_summary | File | ||
| mark_duplicates_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File[] | ||
| per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/3a822294da63b4e19446a285e2fef075e23cf3d0/definitions/pipelines/chipseq.cwl
