Workflow: main-NA12878-platinum-chr20.cwl
Fetched 2024-04-25 11:34:36 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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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 |
|---|---|---|---|
| files | 544a0c25ee0cd6227e34fb58bb1a943a[] | ||
| 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 | 4c0aae05b4c2934d8f6c5d7cd0583f58[] | ||
| reference__snpeff | File[] | ||
| metadata__phenotype | String[] | ||
| config__algorithm__qc | 2b6cd73ef561aa71a7aba663cb0ba806[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| genome_resources__version | Long[] | ||
| reference__genome_context | 2db884fab900840ca8bc20c10bbec62b[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__archive | c04b44965af56121cec50ad53c465a23[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__realign | String[] | ||
| config__algorithm__tools_on | 51b4e8097f2cd548d5e98f2e93d4767c[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__tools_off | 749b0c9a54e56fe1c9bd2b1e0d605c00[] | ||
| config__algorithm__recalibrate | String[] | ||
| config__algorithm__variantcaller | 90a72121f2d49f246ace7c1afbf1beb5[] | ||
| 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/af9a5621efcb44c249697d6df071fe4defe389ac/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/main-NA12878-platinum-chr20.cwl
