Workflow: lobSTR-workflow.cwl

Fetched 2019-12-07 04:16:50 GMT
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Requires:

Inputs

ID Type Title Doc
reference File

lobSTR's bwa reference files

rg-sample String

Use this in the read group SM tag

p1 File[] (Optional)

list of files containing the first end of paired end reads in fasta or fastq format

p2 File[] (Optional)

list of files containing the second end of paired end reads in fasta or fastq format

output_prefix String

prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats

rg-lib String

Use this in the read group LB tag

strinfo File

File containing statistics for each STR.

noise_model File

File to read noise model parameters from (.stepmodel)

Steps

ID Runs Label Doc
allelotype
allelotype.cwl (CommandLineTool)

Run lobSTR allelotype classifier.

samsort
samtools-sort.cwl (CommandLineTool)

Invoke 'samtools sort' (samtools 1.19)

lobSTR
lobSTR-tool.cwl (CommandLineTool)
lobSTR

lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.

samindex
samtools-index.cwl (CommandLineTool)

Invoke 'samtools index' to create a 'BAI' index (samtools 1.19)

Outputs

ID Type Label Doc
vcf File
vcf_stats File
bam_stats File
bam File
Permalink: https://w3id.org/cwl/view/git/767d700e602805112a4c953d166e570cddfa2605/workflows/lobSTR/lobSTR-workflow.cwl