- 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 | f4f13c1a3542862065efbcf049caf6cb[] | ||
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[] | ||
metadata__sex | String[] | ||
rgnames__lane | String[] | ||
reference__rtg | File[] | ||
metadata__batch | https://w3id.org/cwl/salad#null[] | ||
rgnames__sample | String[] | ||
reference__viral | f78f285329f9cf4e229b96b45ae256a4[] | ||
metadata__phenotype | String[] | ||
config__algorithm__qc | e872dd3eaf1af7403ac19dbf4b71a213[] | ||
reference__fasta__base | File[] | ||
reference__bwa__indexes | File[] | ||
genome_resources__version | Long[] | ||
reference__genome_context | a8bc3f155d8907a396de96a13e239eb3[] | ||
config__algorithm__aligner | String[] | ||
config__algorithm__archive | 9bf4eee2fd1c9324aca172594048549a[] | ||
config__algorithm__effects | String[] | ||
config__algorithm__realign | String[] | ||
config__algorithm__svcaller | 2d2c85c2004438b66a0b13a74c408c72[] | ||
config__algorithm__tools_on | 59ea5fce27a622374a91257f1ab6cd8f[] | ||
config__algorithm__validate | https://w3id.org/cwl/salad#null[] | ||
config__algorithm__tools_off | 946ba826ab410b087bc00ba22dcb2f89[] | ||
config__algorithm__recalibrate | String[] | ||
config__algorithm__variantcaller | 7cec1b1b77b55e98be6bd90bfcd714a8[] | ||
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 | https://w3id.org/cwl/salad#null[] | ||
genome_resources__variation__cosmic | https://w3id.org/cwl/salad#null[] | ||
config__algorithm__coverage_interval | https://w3id.org/cwl/salad#null[] | ||
config__algorithm__ensemble__numpass | Long[] | ||
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/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl