Workflow: module-2

Fetched 2021-05-15 11:07:43 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
genome String
indels_1000g File
abra_scratch String
hapmap File
covariates String[]
dbsnp File
runparams https://w3id.org/cwl/view/git/5b6fb984f3cf8e971d677c92a096cd437f34b787/setup/cwl/runparams2cb1eb26-a813-4701-962b-e74c537b5b4e
bams File[]
snps_1000g File
group String

Steps

ID Runs Label Doc
gatk_base_recalibrator
cmo-gatk.BaseRecalibrator/3.3-0/cmo-gatk.BaseRecalibrator.cwl (CommandLineTool)
cmo-gatk-BaseRecalibrator

None

parallel_printreads
gatk_find_covered_intervals
cmo-gatk.FindCoveredIntervals/3.3-0/cmo-gatk.FindCoveredIntervals.cwl (CommandLineTool)
cmo-gatk-FindCoveredIntervals

None

list2bed
cmo-list2bed/1.0.1/cmo-list2bed.cwl (CommandLineTool)
cmo_list2bed

Convert a Picard interval list file to a UCSC BED format

abra
cmo-abra/2.17/cmo-abra.cwl (CommandLineTool)
cmo-abra

None

Outputs

ID Type Label Doc
covint_list File
covint_bed File
outbams File[]
Permalink: https://w3id.org/cwl/view/git/5b6fb984f3cf8e971d677c92a096cd437f34b787/setup/cwl/module-2.cwl