Workflow: main-prealign.cwl
Fetched 2023-01-12 06:46:30 GMT
Verified with cwltool version 3.1.20221201130942
- 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 |
|---|---|---|---|
| files | 9cc97b285c4ea975689209eee020574e[] | ||
| analysis | String[] | ||
| vrn_file | File[] | ||
| resources | String[] | ||
| description | String[] | ||
| genome_build | String[] | ||
| reference__rtg | File[] | ||
| metadata__batch | String[] | ||
| rgnames__sample | String[] | ||
| metadata__phenotype | String[] | ||
| reference__versions | File[] | ||
| config__algorithm__qc | 350166049a79b882196be2f78023e04c[] | ||
| reference__fasta__base | File[] | ||
| reference__snpeff__hg19 | File[] | ||
| reference__genome_context | ebe9eda082ee914d731ba9cccce4f144[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | 907703ba7a6e65f4a41a19d37f7aa7ef[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__ensemble | String[] | ||
| config__algorithm__tools_on | bd35c4d7b1f4a08b093bda74dd049be8[] | ||
| config__algorithm__validate | String[] | ||
| config__algorithm__tools_off | c70b5e3f90e2d1c68a866189aaf81c43[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__variantcaller | Boolean[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__variation__esp | File[] | ||
| genome_resources__variation__lcr | String[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| genome_resources__variation__exac | File[] | ||
| config__algorithm__exclude_regions | 8f8de6afd45d8e7cdbbadc9f335dd085[] | ||
| config__algorithm__variant_regions | File[] | ||
| genome_resources__aliases__ensembl | String[] | ||
| genome_resources__rnaseq__gene_bed | File[] | ||
| genome_resources__variation__1000g | File[] | ||
| genome_resources__variation__dbsnp | File[] | ||
| genome_resources__variation__polyx | String[] | ||
| config__algorithm__nomap_split_size | Long[] | ||
| config__algorithm__validate_regions | String[] | ||
| genome_resources__variation__cosmic | File[] | ||
| config__algorithm__coverage_interval | String[] | ||
| genome_resources__variation__clinvar | File[] | ||
| config__algorithm__min_allele_fraction | Double[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| genome_resources__variation__gnomad_exome | File[] | ||
| genome_resources__variation__train_hapmap | File[] | ||
| genome_resources__variation__train_indels | File[] | ||
| genome_resources__variation__encode_blacklist | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc_to_rec |
steps/qc_to_rec.cwl
(CommandLineTool)
|
||
| variantcall |
wf-variantcall.cwl
(Workflow)
|
||
| prep_samples |
steps/prep_samples.cwl
(CommandLineTool)
|
||
| summarize_vc |
steps/summarize_vc.cwl
(CommandLineTool)
|
||
| multiqc_summary |
steps/multiqc_summary.cwl
(CommandLineTool)
|
||
| organize_noalign |
steps/organize_noalign.cwl
(CommandLineTool)
|
||
| pipeline_summary |
steps/pipeline_summary.cwl
(CommandLineTool)
|
||
| prep_samples_to_rec |
steps/prep_samples_to_rec.cwl
(CommandLineTool)
|
||
| batch_for_variantcall |
steps/batch_for_variantcall.cwl
(CommandLineTool)
|
||
| postprocess_alignment |
steps/postprocess_alignment.cwl
(CommandLineTool)
|
||
| combine_sample_regions |
steps/combine_sample_regions.cwl
(CommandLineTool)
|
||
| postprocess_alignment_to_rec |
steps/postprocess_alignment_to_rec.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| align_bam | File[] | ||
| variants__gvcf | f0d8ac44970e88b5b8d105343fd2f29f[] | ||
| versions__data | File[] | ||
| variants__calls | 18286d6c959faaa2bd5dcbf4568c66cd[] | ||
| versions__tools | File[] | ||
| summary__multiqc | File[] | ||
| rgnames__sample_out | String[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/29c90b75a78ffbd7975c3d39f8e64b137da7450c/prealign/prealign-workflow/main-prealign.cwl
