Workflow: main-NA12878-platinum-chr20.cwl
Fetched 2023-01-10 18:26:49 GMT
Verified with cwltool version 3.1.20221201130942
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | 3d349ac8e726c03cdd56a472c24fb6cd[] | ||
| 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 | 878a1aa237bde2a99c1e4ddae86d09a9[] | ||
| reference__snpeff | File[] | ||
| metadata__phenotype | String[] | ||
| config__algorithm__qc | 9a04def9e8f3533a20ad0965cd924903[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| genome_resources__version | Long[] | ||
| reference__genome_context | 6faf1920dfa6aeec818ce782a99e8218[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__archive | 1daa480e1025fa1a3267bf5bc9f0efa6[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__realign | String[] | ||
| config__algorithm__tools_on | 0fbe686ff39ad5fa3e4333a9882681db[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__tools_off | 3f07a712106795575df0d2dda5bef767[] | ||
| config__algorithm__recalibrate | String[] | ||
| config__algorithm__variantcaller | 645f447273c3970c158590a75b9fc8a9[] | ||
| 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/9606af30d5f047745a1cd7ec1a59d65508ed256e/NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/main-NA12878-platinum-chr20.cwl
