Workflow: LodSeq
Fetched 2023-01-14 22:06:24 GMT
Verified with cwltool version 3.1.20221201130942
LodSeq performs the genetic linkage analysis across families, by computing lod-scores given a gvcf file and a related tfam pedigree file.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/CNRGH/WMS-benchmark/c40ac3f30ea811bffbcf50c5a315212c8673db19/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| vcf | File | ||
| tfam | File | ||
| dom_model | File | ||
| rec_model | File | ||
| out_prefix | String | ||
| chromosomes | String[] | ||
| genetic_maps | Directory | ||
| lod_threshold | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| prepareVCF |
prepareVCF.cwl
(CommandLineTool)
|
prepareVCF |
prepareVCF get .ped and .map files from .vcf and .tfam files and check that all input files and directories exist |
| mergeResults |
merge.cwl
(CommandLineTool)
|
||
| splitByChrom |
splitByChrom.cwl
(CommandLineTool)
|
splitByChrom |
splitByChrom split files (.ped .map) by chromosome |
| prepareGeneticMaps |
prepareGeneticMaps.cwl
(CommandLineTool)
|
prepareGeneticMaps |
prepareGeneticMaps removes header from genetic map file(s) |
| runMultiPointMerlin |
runMultiPointMerlin.cwl
(CommandLineTool)
|
runMultiPointMerlin |
runMultiPointMerlin run multi point merlin analysis |
| runSinglePointMerlin |
runSinglePointMerlin.cwl
(CommandLineTool)
|
runSinglePointMerlin |
runSinglePointMerlin run single point merlin analysis |
| prepareMultiPointFiles |
prepareMultiPointFiles.cwl
(CommandLineTool)
|
prepareMultiPointFiles |
prepareMultiPointFiles prepare multipoint merlin analysis inputs |
| prepareSinglePointFiles |
prepareSinglePointFiles.cwl
(CommandLineTool)
|
prepareSinglePointFiles |
prepareSinglePointFiles prepare single point merlin analysis inputs |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| out_dir | Directory | ||
| out_dir_mr | Directory | ||
| out_dir_pgm | Directory[] | ||
| out_dir_pmf | Directory[] | ||
| out_dir_psf | Directory[] | ||
| out_dir_rmm | Directory[] | ||
| out_dir_rsm | Directory[] | ||
| out_dir_sbc | Directory[] |
Permalink:
https://w3id.org/cwl/view/git/c40ac3f30ea811bffbcf50c5a315212c8673db19/workflows/cwltoil/lodseq.cwl
