Workflow: create_diploid_genome.cwl
Fetched 2024-04-26 12:16:18 GMT
Verified with cwltool version 3.1.20221201130942
Diploid Genome Creation Workflow
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| REF_NAME | String | ||
| NUM_CORES | Integer | ||
| SED_STRING1 | String | ||
| SED_STRING2 | String | ||
| INPUT_GTF_FILE | File | ||
| INPUT_VCF_FILE1 | File | ||
| INPUT_VCF_FILE2 | File | ||
| HAPOLID_COPY_NAME | String | ||
| GTF_SUFFIX_STRING1 | String | ||
| GTF_SUFFIX_STRING2 | String | ||
| INPUT_HAPLOID_FILE | File | ||
| VARIANT_HAPLOID_FILE1 | String | ||
| VARIANT_HAPLOID_FILE2 | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index_vcf1 |
../genome_create/cwl/index_vcf.cwl
(CommandLineTool)
|
Index VCF file |
|
| index_vcf2 |
../genome_create/cwl/index_vcf.cwl
(CommandLineTool)
|
Index VCF file |
|
| tar_create |
../genome_create/cwl/tar_create.cwl
(CommandLineTool)
|
command line: tar |
|
| copy_genome |
../genome_create/cwl/copy_genome.cwl
(CommandLineTool)
|
Make copy of genome |
|
| combine_gtfs |
../genome_create/cwl/combine_gtfs.cwl
(CommandLineTool)
|
Combine gtf files |
|
| add_variants1 |
../genome_create/cwl/add_variants.cwl
(CommandLineTool)
|
Add variants to fasta files |
|
| add_variants2 |
../genome_create/cwl/add_variants.cwl
(CommandLineTool)
|
Add variants to fasta files |
|
| combine_fastas |
../genome_create/cwl/combine_fastas.cwl
(CommandLineTool)
|
Combine fasta files |
|
| prepare_reference |
../genome_create/cwl/prepare_reference.cwl
(CommandLineTool)
|
Create diploid reference files |
|
| rename_gtf_features1 |
../genome_create/cwl/rename_gtf_features1.cwl
(CommandLineTool)
|
Changing gene, transcript, and chromosome names in GTF |
|
| rename_gtf_features2 |
../genome_create/cwl/rename_gtf_features2.cwl
(CommandLineTool)
|
Changing gene, transcript, and chromosome names in GTF |
|
| rename_fasta_features1 |
../genome_create/cwl/rename_fasta_features1.cwl
(CommandLineTool)
|
Changing chromosome names in genome for diploid version |
|
| rename_fasta_features2 |
../genome_create/cwl/rename_fasta_features2.cwl
(CommandLineTool)
|
Changing chromosome names in genome for diploid version |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| OUTPUT | File[] |
Permalink:
https://w3id.org/cwl/view/git/f621d09c48a6abfd2c63105a2c096f39a1627a07/workflow/create_diploid_genome.cwl
