- 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 | 1b5012781a3e1e2c8f17bdd2f47bbe32[] | ||
analysis | String[] | ||
vrn_file | File[] | ||
resources | String[] | ||
description | String[] | ||
genome_build | String[] | ||
reference__rtg | File[] | ||
metadata__batch | String[] | ||
rgnames__sample | String[] | ||
reference__twobit | File[] | ||
metadata__phenotype | String[] | ||
config__algorithm__qc | da340ce8486fae6093cb18fbd8a11fc2[] | ||
reference__fasta__base | File[] | ||
reference__snpeff__hg19 | File[] | ||
reference__genome_context | 6dc7f19efe018bcdfbdfb1845c0326a5[] | ||
config__algorithm__effects | String[] | ||
config__algorithm__vcfanno | 0b8b6e02ea4b16e1dccccf57e1bbee81[] | ||
config__algorithm__coverage | File[] | ||
config__algorithm__ensemble | String[] | ||
config__algorithm__tools_on | d5b028826cdcd1dec530d57b788c4e2c[] | ||
config__algorithm__validate | String[] | ||
config__algorithm__tools_off | 3d835593eb4dc6a505e24f3e41eeb136[] | ||
config__algorithm__recalibrate | Boolean[] | ||
config__algorithm__variantcaller | Boolean[] | ||
genome_resources__aliases__human | Boolean[] | ||
genome_resources__variation__esp | File[] | ||
genome_resources__variation__lcr | String[] | ||
genome_resources__aliases__snpeff | String[] | ||
genome_resources__variation__exac | File[] | ||
config__algorithm__exclude_regions | af58d2e581b0a5e82049c7646ef89db5[] | ||
config__algorithm__variant_regions | File[] | ||
genome_resources__aliases__ensembl | String[] | ||
genome_resources__rnaseq__gene_bed | File[] | ||
genome_resources__variation__1000g | File[] | ||
genome_resources__variation__dbsnp | File[] | ||
genome_resources__variation__polyx | String[] | ||
config__algorithm__nomap_split_size | Long[] | ||
config__algorithm__validate_regions | String[] | ||
genome_resources__variation__cosmic | File[] | ||
config__algorithm__coverage_interval | String[] | ||
genome_resources__variation__clinvar | File[] | ||
config__algorithm__min_allele_fraction | Long[] | ||
config__algorithm__nomap_split_targets | Long[] | ||
genome_resources__variation__train_hapmap | File[] | ||
genome_resources__variation__train_indels | File[] | ||
genome_resources__variation__encode_blacklist | String[] |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
qc_to_rec |
steps/qc_to_rec.cwl
(CommandLineTool)
|
||
variantcall |
wf-variantcall.cwl
(Workflow)
|
||
prep_samples |
steps/prep_samples.cwl
(CommandLineTool)
|
||
summarize_vc |
steps/summarize_vc.cwl
(CommandLineTool)
|
||
multiqc_summary |
steps/multiqc_summary.cwl
(CommandLineTool)
|
||
organize_noalign |
steps/organize_noalign.cwl
(CommandLineTool)
|
||
pipeline_summary |
steps/pipeline_summary.cwl
(CommandLineTool)
|
||
prep_samples_to_rec |
steps/prep_samples_to_rec.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[] | ||
variants__gvcf | 2488270d9a566d79e3ec197d530b6755[] | ||
variants__calls | d895f2c942baeb12cef287861d28d0b8[] | ||
summary__multiqc | File[] | ||
rgnames__sample_out | String[] | ||
regions__sample_callable | File[] | ||
validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/8541da9674f17a2f44bd4cb042a3c8a2bbd22e5d/prealign/prealign-workflow/main-prealign.cwl