Workflow: main-SGDP-recall.cwl
Fetched 2023-01-04 02:28:37 GMT
Verified with cwltool version 3.1.20221201130942
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source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | 8e0f489b37a6a2463e01acbda73f9599[] | ||
| analysis | String[] | ||
| vrn_file | https://w3id.org/cwl/salad#null[] | ||
| description | String[] | ||
| rgnames__lb | https://w3id.org/cwl/salad#null[] | ||
| rgnames__pl | String[] | ||
| rgnames__pu | String[] | ||
| rgnames__rg | String[] | ||
| genome_build | String[] | ||
| metadata__sex | String[] | ||
| rgnames__lane | String[] | ||
| reference__rtg | File[] | ||
| metadata__batch | https://w3id.org/cwl/salad#null[] | ||
| rgnames__sample | String[] | ||
| reference__viral | 76232135cb9b8340588e4846b3bc1dfc[] | ||
| metadata__phenotype | String[] | ||
| config__algorithm__qc | dfdbfdf339291c8e2da489b7bccdc839[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| genome_resources__version | Long[] | ||
| reference__genome_context | 0ae48b81f0307b8ae49f5b0ff5b51e39[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__archive | 2987f6f113d6528daec78e6120331f43[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__realign | String[] | ||
| config__algorithm__svcaller | 31c94ae46a7de3a9f795a83897de90f4[] | ||
| config__algorithm__tools_on | c002808104fff1f2c14070559f300b93[] | ||
| config__algorithm__validate | https://w3id.org/cwl/salad#null[] | ||
| config__algorithm__tools_off | e1727612b4069b6878645c47e5470969[] | ||
| config__algorithm__recalibrate | String[] | ||
| config__algorithm__variantcaller | 2c0327aeba00a0e90ea4c8619010df1e[] | ||
| genome_resources__aliases__human | String[] | ||
| genome_resources__rnaseq__dexseq | File[] | ||
| genome_resources__variation__lcr | File[] | ||
| genome_resources__aliases__snpeff | String[] | ||
| genome_resources__rnaseq__refflat | File[] | ||
| config__algorithm__mark_duplicates | String[] | ||
| config__algorithm__variant_regions | https://w3id.org/cwl/salad#null[] | ||
| genome_resources__aliases__ensembl | String[] | ||
| genome_resources__variation__dbsnp | File[] | ||
| config__algorithm__align_split_size | https://w3id.org/cwl/salad#null[] | ||
| config__algorithm__nomap_split_size | Long[] | ||
| config__algorithm__validate_regions | https://w3id.org/cwl/salad#null[] | ||
| genome_resources__variation__cosmic | https://w3id.org/cwl/salad#null[] | ||
| config__algorithm__coverage_interval | https://w3id.org/cwl/salad#null[] | ||
| config__algorithm__ensemble__numpass | Long[] | ||
| genome_resources__rnaseq__transcripts | File[] | ||
| config__algorithm__nomap_split_targets | Long[] | ||
| genome_resources__variation__sv_repeat | File[] | ||
| genome_resources__variation__qsignature | File[] | ||
| genome_resources__variation__train_omni | File[] | ||
| genome_resources__variation__train_1000g | File[] | ||
| genome_resources__variation__train_hapmap | File[] | ||
| genome_resources__variation__train_indels | File[] | ||
| genome_resources__rnaseq__transcripts_mask | File[] | ||
| genome_resources__rnaseq__transcriptome_index__tophat | String[] |
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)
|
||
| 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)
|
||
| summarize_grading_vc |
steps/summarize_grading_vc.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[] | ||
| summary__multiqc | File[] | ||
| validate__grading_summary | File[] |
Permalink:
https://w3id.org/cwl/view/git/c4592973b1580e3ff44cb697f64b12345b91e6f5/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl
