Workflow: exome alignment and germline variant detection
Fetched 2025-11-02 06:33:22 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 |
|---|---|---|---|
| ploidy | Integer (Optional) | ||
| omni_vcf | File | ||
| sequence | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/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/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
| intervals | ed4ea0635ea3cda60e7522edbc59dccf[] | ||
| reference | File | ||
| gvcf_gq_bands | String[] | ||
| synonyms_file | File (Optional) | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] (Optional) | ||
| bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
|
| target_intervals | File | ||
| summary_intervals | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/labelled_file.yml#labelled_file[] | ||
| per_base_intervals | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/labelled_file.yml#labelled_file[] | ||
| per_target_intervals | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/labelled_file.yml#labelled_file[] | ||
| qc_minimum_base_quality | Integer (Optional) | ||
| emit_reference_confidence | |||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| generate_gvcfs | scatter GATK HaplotypeCaller over intervals | ||
| extract_freemix |
germline_exome_gvcf.cwl#extract_freemix/e01b7b7b-a7e8-4b1d-b5c2-83859127e78b
(ExpressionTool)
|
||
| alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| gvcf | File[] | ||
| flagstats | File | ||
| hs_metrics | File | ||
| summary_hs_metrics | File[] | ||
| insert_size_metrics | File | ||
| per_base_hs_metrics | File[] | ||
| verify_bam_id_depth | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File[] | ||
| verify_bam_id_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/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/pipelines/germline_exome_gvcf.cwl
