- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
files | 78c3256ba304f1ebcc4f15e7f7e008f8[] | ||
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 | 173ed01d472dd9611cca900e82a03535[] | ||
metadata__phenotype | String[] | ||
config__algorithm__qc | f38cea62fd1f41496a4e6d1d0b923eb5[] | ||
reference__fasta__base | File[] | ||
reference__bwa__indexes | File[] | ||
genome_resources__version | Long[] | ||
reference__genome_context | 59c2871b41d88cc56682398cb0016ae2[] | ||
config__algorithm__aligner | String[] | ||
config__algorithm__archive | 8c7e2fa118fa7e68cc741eac9bb52c06[] | ||
config__algorithm__effects | String[] | ||
config__algorithm__realign | String[] | ||
config__algorithm__svcaller | b21a2ba86f2c9c5db341ed2630ed5766[] | ||
config__algorithm__tools_on | b2753a93ac46152c3f648839ad3bdd16[] | ||
config__algorithm__validate | https://w3id.org/cwl/salad#null[] | ||
config__algorithm__tools_off | 4ee189c7dbfe39bd5c79aef72942f491[] | ||
config__algorithm__recalibrate | String[] | ||
config__algorithm__variantcaller | 3442e1359f5832fdd1e6b6fb5e2c2102[] | ||
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/9606af30d5f047745a1cd7ec1a59d65508ed256e/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl