Workflow: module-1-2-chunk

Fetched 2023-01-12 06:05:12 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
dbsnp File
group String
cosmic File
fastq1 0332530acecac8250a32aa71addd5b76[]
fastq2 caf524a7b218d8ca0a5b478f873761a8[]
genome String
hapmap File
refseq File
adapter String[]
tmp_dir String
adapter2 String[]
add_rg_CN String[]
add_rg_ID a5c298f8512d61d87bb75bb6f7930f37[]
add_rg_LB String[]
add_rg_PL String[]
add_rg_PU 3c99f0fdfc2cbb099bdd25497dfa0b16[]
add_rg_SM String[]
intervals String (Optional)
mutect_rf String[]
runparams
bwa_output String[]
covariates String[]
snps_1000g File
mutect_dcov Integer
abra_scratch String
indels_1000g File
opt_dup_pix_dist String

Steps

ID Runs Label Doc
mapping module-1-scatter-chunk
realignment
module-2.cwl (Workflow)
module-2

Outputs

ID Type Label Doc
bams File[]
clstats1 16edae261a3d325cb1e3142e6d3a81af[]
clstats2 d34b4ffa67cb56bcab743bc3a4c07ab2[]
covint_bed File
md_metrics File[]
covint_list File
Permalink: https://w3id.org/cwl/view/git/3ec29bfdcbc444c6599e484640cf83a7c5d91aaa/setup/cwl/module-1-2.chunk.cwl