- 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 | 6dd6f6f0149ed8b5c657b0396114f6e6[] | ||
analysis | String[] | ||
vrn_file | String[] | ||
resources | String[] | ||
description | String[] | ||
rgnames__lb | String[] | ||
rgnames__pl | String[] | ||
rgnames__pu | String[] | ||
rgnames__rg | String[] | ||
genome_build | String[] | ||
rgnames__lane | String[] | ||
reference__rtg | File[] | ||
metadata__batch | String[] | ||
rgnames__sample | String[] | ||
reference__twobit | File[] | ||
metadata__phenotype | String[] | ||
config__algorithm__qc | 733485f1dbe617e79e29f686de06fe0e[] | ||
reference__fasta__base | File[] | ||
reference__genome_context | e432b38bea6d844b466912e86172fbab[] | ||
config__algorithm__aligner | String[] | ||
config__algorithm__effects | Boolean[] | ||
config__algorithm__adapters | 4569971ce7572941e5c4f0473ea6228a[] | ||
config__algorithm__tools_on | da796332f9689540ddd219e5bf2a037f[] | ||
config__algorithm__validate | File[] | ||
config__algorithm__bam_clean | Boolean[] | ||
config__algorithm__tools_off | e58a86a212403f04e04a582f9e981f09[] | ||
reference__minimap2__indexes | fa2b44120b9b2d91238ce7c84ffc7e4e[] | ||
reference__snpeff__GRCh37_75 | File[] | ||
config__algorithm__trim_reads | Boolean[] | ||
config__algorithm__recalibrate | Boolean[] | ||
config__algorithm__variantcaller | 7e0c455c70b0b51c7da300b3562a7e1c[] | ||
genome_resources__aliases__human | Boolean[] | ||
genome_resources__variation__lcr | File[] | ||
genome_resources__aliases__snpeff | String[] | ||
config__algorithm__exclude_regions | cdd82b8b0855d81ff1339a4f56c5bcc4[] | ||
config__algorithm__mark_duplicates | Boolean[] | ||
config__algorithm__variant_regions | File[] | ||
genome_resources__aliases__ensembl | String[] | ||
genome_resources__rnaseq__gene_bed | File[] | ||
genome_resources__variation__dbsnp | File[] | ||
genome_resources__variation__polyx | File[] | ||
config__algorithm__align_split_size | String[] | ||
config__algorithm__nomap_split_size | Long[] | ||
config__algorithm__validate_regions | File[] | ||
genome_resources__variation__cosmic | File[] | ||
config__algorithm__coverage_interval | String[] | ||
config__algorithm__nomap_split_targets | Long[] | ||
genome_resources__variation__train_hapmap | File[] | ||
genome_resources__variation__train_indels | File[] | ||
genome_resources__variation__encode_blacklist | File[] |
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)
|
||
summarize_vc |
steps/summarize_vc.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)
|
||
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 | 93a9016894089a0fafa5db0760cafd16[] | ||
variants__calls | 979b092432f9ee7a82b5cfa14d164fcc[] | ||
summary__multiqc | File[] | ||
rgnames__sample_out | String[] | ||
regions__sample_callable | File[] | ||
validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/af9a5621efcb44c249697d6df071fe4defe389ac/somatic-lowfreq/pisces-titr-workflow/main-pisces-titr.cwl