- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
---|---|---|---|
sequence | https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/sequence_data.yml#sequence_data[] | sequence: sequencing data and readgroup information |
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. |
trimming | https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
reference | File | ||
final_name | String (Optional) | ||
bait_intervals | File | ||
target_intervals | File | ||
summary_intervals | https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/labelled_file.yml#labelled_file[] | ||
per_base_intervals | https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/labelled_file.yml#labelled_file[] | ||
per_target_intervals | https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/labelled_file.yml#labelled_file[] | ||
qc_minimum_base_quality | Integer (Optional) | ||
qc_minimum_mapping_quality | Integer (Optional) | ||
picard_metric_accumulation_level | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
qc |
../subworkflows/qc_exome_no_verify_bam.cwl
(Workflow)
|
Exome QC workflow | |
alignment | Alignment without BQSR |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
bam | File | ||
flagstats | File | ||
hs_metrics | File | ||
summary_hs_metrics | File[] | ||
insert_size_metrics | File | ||
per_base_hs_metrics | File[] | ||
insert_size_histogram | File | ||
per_target_hs_metrics | 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/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/pipelines/alignment_exome_nonhuman.cwl