- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
files | 9a65268ef4c02f15482ab7ed39a45de0[] | ||
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 | 14822bf0a4371d0fc438657f31739668[] | ||
reference__fasta__base | File[] | ||
reference__genome_context | a30a774c0144e5c2a39126b0f5da82de[] | ||
config__algorithm__aligner | String[] | ||
config__algorithm__effects | Boolean[] | ||
config__algorithm__adapters | feb377e92b22bb3ca5c1efede5ff1c6e[] | ||
config__algorithm__tools_on | daf9194e50b77a211da2ec05e117f9cf[] | ||
config__algorithm__validate | File[] | ||
config__algorithm__bam_clean | Boolean[] | ||
config__algorithm__tools_off | 7025aa4e54de789b3408d597f6757261[] | ||
reference__minimap2__indexes | eec549ee156ce72054bd3c91b941c5cf[] | ||
reference__snpeff__GRCh37_75 | File[] | ||
config__algorithm__trim_reads | Boolean[] | ||
config__algorithm__recalibrate | Boolean[] | ||
config__algorithm__variantcaller | 75c6879cb361781e2d97d59c1884cddf[] | ||
genome_resources__aliases__human | Boolean[] | ||
genome_resources__variation__lcr | File[] | ||
genome_resources__aliases__snpeff | String[] | ||
config__algorithm__exclude_regions | 4973115fc6be7ebc5c1167d887f01d1d[] | ||
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 | fd0936b5d7da48edc720ce214f54dc95[] | ||
variants__calls | 9610a2f39a57bcb60e8c404280ea235c[] | ||
summary__multiqc | File[] | ||
rgnames__sample_out | String[] | ||
regions__sample_callable | File[] | ||
validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/c4592973b1580e3ff44cb697f64b12345b91e6f5/somatic-lowfreq/pisces-titr-workflow/main-pisces-titr.cwl