- 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 |
---|---|---|---|
ploidy | Integer (Optional) | ||
omni_vcf | File | ||
sequence | https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/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/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
intervals | 8de925be85f892dcbf2a411b9844262e[] | ||
reference | File | ||
qc_intervals | File | ||
gvcf_gq_bands | String[] | ||
synonyms_file | File (Optional) | ||
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. |
|
summary_intervals | https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/labelled_file.yml#labelled_file[] | ||
per_base_intervals | https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/labelled_file.yml#labelled_file[] | ||
annotate_coding_only | Boolean (Optional) | ||
minimum_base_quality | Integer (Optional) | ||
per_target_intervals | https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/labelled_file.yml#labelled_file[] | ||
minimum_mapping_quality | Integer (Optional) | ||
emit_reference_confidence | |||
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_wgs_gvcf.cwl#extract_freemix/cb3dbc4b-05b7-4394-bf0f-16602fa86364
(ExpressionTool)
|
||
alignment_and_qc |
alignment_wgs.cwl
(Workflow)
|
wgs alignment with qc |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
cram | File | ||
gvcf | File[] | ||
flagstats | File | ||
wgs_metrics | File | ||
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/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/pipelines/germline_wgs_gvcf.cwl