Workflow: exomeseq-gatk4-01-preprocessing.cwl

Fetched 2021-05-14 19:06:54 GMT
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Inputs

ID Type Title Doc
intervals File[] (Optional)
interval_padding Integer (Optional)
read_pair https://w3id.org/cwl/view/git/bbe24d8d7fde2e918583b96805909a2867b749d6/types/FASTQReadPairType.yml#FASTQReadPairType
library String
reference_genome File
threads Integer
bait_interval_list File
target_interval_list File
known_sites File[]
resource_dbsnp File
platform String

Steps

ID Runs Label Doc
qc
../tools/fastqc.cwl (CommandLineTool)
trim
../tools/trim_galore.cwl (CommandLineTool)
file_pair_details
../tools/extract-named-file-pair-details.cwl (ExpressionTool)
Given a FASTQReadPairType returns a 2D array of the files contained within
recalibrate_02_apply_bqsr
../tools/GATK4-ApplyBQSR.cwl (CommandLineTool)
combine_reads
../tools/concat-gz-files.cwl (CommandLineTool)
variant_calling
../tools/GATK4-HaplotypeCaller.cwl (CommandLineTool)
generate_sample_filenames
../tools/generate-sample-filenames.cwl (ExpressionTool)
Generates a set of file names for preprocessing steps based on an input sample name
sort
../tools/GATK4-SortSam.cwl (CommandLineTool)
recalibrate_01_analyze
../tools/GATK4-BaseRecalibrator.cwl (CommandLineTool)
mark_duplicates
../tools/GATK4-MarkDuplicates.cwl (CommandLineTool)
map
../tools/gitc-bwa-mem-samtools.cwl (CommandLineTool)

Outputs

ID Type Label Doc
recalibrated_reads File
raw_variants File

VCF file from per sample variant calling

trim_reports File[]
markduplicates_bam File
recalibration_table File
haplotypes_bam File

BAM file containing assembled haplotypes and locally realigned reads

fastqc_reports File[]
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