Workflow: main-prealign.cwl
Fetched 2023-01-12 04:00:34 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 | fe86b5b23d3c8aace8565b8aa6d36623[] | ||
| analysis | String[] | ||
| vrn_file | File[] | ||
| resources | String[] | ||
| description | String[] | ||
| genome_build | String[] | ||
| reference__rtg | File[] | ||
| metadata__batch | String[] | ||
| rgnames__sample | String[] | ||
| reference__twobit | File[] | ||
| metadata__phenotype | String[] | ||
| config__algorithm__qc | 8c9dbdc8a873f5267e8b1ab933041656[] | ||
| reference__fasta__base | File[] | ||
| reference__snpeff__hg19 | File[] | ||
| reference__genome_context | 088c636d8b70000b3a430375ba88b9fa[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | 264234ed5a13cf67acfb22029ef62a54[] | ||
| config__algorithm__coverage | File[] | ||
| config__algorithm__ensemble | String[] | ||
| config__algorithm__tools_on | 4dbc356b642a79d795edbc0a89d7c323[] | ||
| config__algorithm__validate | String[] | ||
| config__algorithm__tools_off | 4e3ec8201c4f09605fb95ff6a708f642[] | ||
| 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 | 2a0ed861fb3c462acf7203b830295df5[] | ||
| 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 | Long[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| 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 | d41793c59f13f9b2eb04f4bebaebaafd[] | ||
| variants__calls | 4fd98e313c88cdb3c47d4903868eea80[] | ||
| summary__multiqc | File[] | ||
| rgnames__sample_out | String[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/48ca2661644e01e2d4b7f8ad8f2588a31cf87537/prealign/prealign-workflow/main-prealign.cwl
