Workflow: main-wes_chr21_test.cwl
Fetched 2023-08-16 22:21:53 GMT
Verified with cwltool version 3.1.20230201224320
- 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 | a562edb8b10ef30bee34fa59f5e576eb[] | ||
| 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__viral | File[] | ||
| metadata__phenotype | String[] | ||
| reference__versions | File[] | ||
| config__algorithm__qc | 5eb988d136f266fc8ccec2cc6070f9f6[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| reference__genome_context | eeebee4582105cf8e14c35e6e4f1752b[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__archive | String[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__vcfanno | 79ed99bc66a47a20c3ba9047779847cf[] | ||
| config__algorithm__adapters | a9acd89927171112ebcee1c43596523a[] | ||
| config__algorithm__ensemble | String[] | ||
| config__algorithm__svcaller | 60010bae36f4ce46ae4724b87529eda3[] | ||
| config__algorithm__tools_on | 1d83fb6a0f17ede3e610129d87cb5e8a[] | ||
| config__algorithm__validate | File[] | ||
| config__algorithm__bam_clean | Boolean[] | ||
| config__algorithm__tools_off | 52f78147fe7cd3489264208cb66cde7f[] | ||
| reference__snpeff__GRCh37_75 | File[] | ||
| config__algorithm__svvalidate | String[] | ||
| config__algorithm__trim_reads | String[] | ||
| config__algorithm__recalibrate | Boolean[] | ||
| config__algorithm__svprioritize | String[] | ||
| config__algorithm__variantcaller | 1bdfcf4692e5c79c73168c61ead2667c[] | ||
| genome_resources__aliases__human | Boolean[] | ||
| genome_resources__variation__esp | File[] | ||
| genome_resources__variation__lcr | File[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| genome_resources__variation__exac | File[] | ||
| config__algorithm__exclude_regions | 3a4fd90f375e687a1b0bec13905189d7[] | ||
| config__algorithm__mark_duplicates | Boolean[] | ||
| 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 | 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[] | ||
| genome_resources__variation__clinvar | File[] | ||
| config__algorithm__min_allele_fraction | Double[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| genome_resources__variation__gc_profile | String[] | ||
| genome_resources__variation__gnomad_exome | String[] | ||
| genome_resources__variation__train_hapmap | File[] | ||
| genome_resources__variation__train_indels | File[] | ||
| genome_resources__variation__encode_blacklist | File[] | ||
| genome_resources__variation__germline_het_pon | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| svcall |
wf-svcall.cwl
(Workflow)
|
||
| alignment |
wf-alignment.cwl
(Workflow)
|
||
| qc_to_rec |
steps/qc_to_rec.cwl
(CommandLineTool)
|
||
| variantcall |
wf-variantcall.cwl
(Workflow)
|
||
| batch_for_sv |
steps/batch_for_sv.cwl
(CommandLineTool)
|
||
| prep_samples |
steps/prep_samples.cwl
(CommandLineTool)
|
||
| summarize_sv |
steps/summarize_sv.cwl
(CommandLineTool)
|
||
| summarize_vc |
steps/summarize_vc.cwl
(CommandLineTool)
|
||
| combine_calls |
steps/combine_calls.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)
|
||
| calculate_sv_bins |
steps/calculate_sv_bins.cwl
(CommandLineTool)
|
||
| batch_for_ensemble |
steps/batch_for_ensemble.cwl
(CommandLineTool)
|
||
| prep_samples_to_rec |
steps/prep_samples_to_rec.cwl
(CommandLineTool)
|
||
| batch_for_variantcall |
steps/batch_for_variantcall.cwl
(CommandLineTool)
|
||
| calculate_sv_coverage |
steps/calculate_sv_coverage.cwl
(CommandLineTool)
|
||
| normalize_sv_coverage |
steps/normalize_sv_coverage.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[] | ||
| sv__calls | d18e9b4a9901a5b3355a1309693194e0[] | ||
| variants__gvcf | 608e3c683adb54f21b44ac19587832d1[] | ||
| versions__data | File[] | ||
| variants__calls | efdacb60e7f38bf9ddc61bbd586a75f1[] | ||
| versions__tools | File[] | ||
| summary__multiqc | File[] | ||
| sv__supplemental | c0ea81c621641eff044ff11750ceed4c[] | ||
| rgnames__sample_out | String[] | ||
| sv__prioritize__raw | 87964cf757a241f7cf4524d67c41a632[] | ||
| sv__prioritize__tsv | c6692216e206b3293b84ff7d34bc4799[] | ||
| regions__sample_callable | File[] | ||
| validate__grading_summary | File[] | ||
| svvalidate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/af9a5621efcb44c249697d6df071fe4defe389ac/wes-agha-test/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
