Workflow: main-NA12878-platinum-chr20.cwl
Fetched 2023-01-12 06:47:11 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 | ffc19f035b1649cf06f8b7495002afa8[] | ||
| analysis | String[] | ||
| vrn_file | https://w3id.org/cwl/salad#null[] | ||
| description | String[] | ||
| rgnames__lb | https://w3id.org/cwl/salad#null[] | ||
| rgnames__pl | String[] | ||
| rgnames__pu | String[] | ||
| rgnames__rg | String[] | ||
| genome_build | String[] | ||
| rgnames__lane | String[] | ||
| reference__rtg | File[] | ||
| metadata__batch | https://w3id.org/cwl/salad#null[] | ||
| rgnames__sample | String[] | ||
| reference__viral | 9bf9cdf9c092d9b908fa1bd4bc73ae93[] | ||
| reference__snpeff | File[] | ||
| metadata__phenotype | String[] | ||
| config__algorithm__qc | 501f78890d9688e3a5ff80c263c64dd7[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| genome_resources__version | Long[] | ||
| reference__genome_context | c19ebc1177e7b0e1859a6ad77c48f5ea[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__archive | 5f3c74afd6355093ef567d6a55c164cb[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__realign | String[] | ||
| config__algorithm__tools_on | 0daa52b502a701fd197ca5b0cc1f8746[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__tools_off | 22b0bab58cf6f00994e1d555366e51e3[] | ||
| config__algorithm__recalibrate | String[] | ||
| config__algorithm__variantcaller | aa7e5dcd525e603e22bf7cb084b075cb[] | ||
| genome_resources__aliases__human | String[] | ||
| genome_resources__rnaseq__dexseq | File[] | ||
| genome_resources__variation__lcr | File[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| genome_resources__rnaseq__refflat | File[] | ||
| config__algorithm__mark_duplicates | String[] | ||
| config__algorithm__variant_regions | https://w3id.org/cwl/salad#null[] | ||
| genome_resources__aliases__ensembl | String[] | ||
| genome_resources__variation__dbsnp | File[] | ||
| config__algorithm__align_split_size | https://w3id.org/cwl/salad#null[] | ||
| config__algorithm__nomap_split_size | Long[] | ||
| config__algorithm__validate_regions | File[] | ||
| genome_resources__variation__cosmic | https://w3id.org/cwl/salad#null[] | ||
| config__algorithm__coverage_interval | https://w3id.org/cwl/salad#null[] | ||
| genome_resources__rnaseq__transcripts | File[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| genome_resources__variation__sv_repeat | File[] | ||
| genome_resources__variation__qsignature | File[] | ||
| genome_resources__variation__train_omni | File[] | ||
| genome_resources__variation__train_1000g | File[] | ||
| genome_resources__variation__train_hapmap | File[] | ||
| genome_resources__variation__train_indels | File[] | ||
| genome_resources__rnaseq__transcripts_mask | File[] | ||
| genome_resources__rnaseq__transcriptome_index__tophat | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| alignment |
wf-alignment.cwl
(Workflow)
|
||
| qc_to_rec |
steps/qc_to_rec.cwl
(CommandLineTool)
|
||
| variantcall |
wf-variantcall.cwl
(Workflow)
|
||
| prep_samples |
steps/prep_samples.cwl
(CommandLineTool)
|
||
| multiqc_summary |
steps/multiqc_summary.cwl
(CommandLineTool)
|
||
| alignment_to_rec |
steps/alignment_to_rec.cwl
(CommandLineTool)
|
||
| pipeline_summary |
steps/pipeline_summary.cwl
(CommandLineTool)
|
||
| prep_samples_to_rec |
steps/prep_samples_to_rec.cwl
(CommandLineTool)
|
||
| summarize_grading_vc |
steps/summarize_grading_vc.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[] | ||
| summary__multiqc | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/main-NA12878-platinum-chr20.cwl
