Workflow: main-SGDP-recall.cwl
Fetched 2023-01-11 21:13:04 GMT
Verified with cwltool version 3.1.20221201130942
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Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| files | 69fa3b5781cd1131afbf671e64f21ba5[] | ||
| 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 | a1ca4a315d31fd6a43b91e745c3e8c16[] | ||
| metadata__phenotype | String[] | ||
| config__algorithm__qc | c48cdc68e9a9b39409b3716f339a31ca[] | ||
| reference__fasta__base | File[] | ||
| reference__bwa__indexes | File[] | ||
| genome_resources__version | Long[] | ||
| reference__genome_context | 8e7a91a7c6c6c537918c61e1de8addd8[] | ||
| config__algorithm__aligner | String[] | ||
| config__algorithm__archive | e53af44b2164286325b6ffc39e277fec[] | ||
| config__algorithm__effects | String[] | ||
| config__algorithm__realign | String[] | ||
| config__algorithm__svcaller | b564d03ba83af367a565516de2bcf704[] | ||
| config__algorithm__tools_on | 9d168154f29102edd989614a34be7426[] | ||
| config__algorithm__validate | https://w3id.org/cwl/salad#null[] | ||
| config__algorithm__tools_off | e4f61c36d7fd53de9145ed83cb3fc965[] | ||
| config__algorithm__recalibrate | String[] | ||
| config__algorithm__variantcaller | ddec8ed43310a3de07edd6fd6157c35d[] | ||
| 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/d7e640fb2359b4e81be071ad65af2730ad25d0bb/SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl
