Workflow: Chipseq alignment with qc and creating homer tag directory
Fetched 2023-01-09 13:03:01 GMT
Verified with cwltool version 3.1.20221201130942
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Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| omni_vcf | File | ||
| intervals | File | ||
| reference | File | ||
| final_name | String (Optional) | ||
| bqsr_intervals | String[] | ||
| bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
|
| chipseq_sequence | https://w3id.org/cwl/view/git/fbeea265295ae596d5a3ba563e766be0c4fc26e8/definitions/types/sequence_data.yml#sequence_data[] | chipseq_sequence: sequencing data and readgroup information |
chipseq_sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| summary_intervals | https://w3id.org/cwl/view/git/fbeea265295ae596d5a3ba563e766be0c4fc26e8/definitions/types/labelled_file.yml#labelled_file[] | ||
| per_base_intervals | https://w3id.org/cwl/view/git/fbeea265295ae596d5a3ba563e766be0c4fc26e8/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/fbeea265295ae596d5a3ba563e766be0c4fc26e8/definitions/types/labelled_file.yml#labelled_file[] | ||
| 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 |
homer annotation data is too large to include in the docker image, so it requires a directory to be mounted at /opt/homerdata/ containing - config.txt - homer configuration file with directories pointing to paths like \"data/accession\" - data - folder containing homer annotation data files at WUSTL, this can be provided by providing the following in an analysis-project configuration: docker_volumes: \"/gscmnt/gc2560/core/annotation_data/homer:/opt/homerdata\" or outside the pipelines: LSF_DOCKER_VOLUMES=\"$LSF_DOCKER_VOLUMES /gscmnt/gc2560/core/annotation_data/homer:/opt/homerdata\" for compute1, instead use the path `/storage1/fs1/bga/Active/gmsroot/gc2560/core/annotation_data/homer` |
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[] |
https://w3id.org/cwl/view/git/fbeea265295ae596d5a3ba563e766be0c4fc26e8/definitions/pipelines/chipseq.cwl
