Workflow: test-workflow

Fetched 2019-06-27 13:02:04 GMT
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Inputs

ID Type Title Doc
sra_run_ids String[]

A list of SRA Run ID such as ERR034597

ref String

name of reference (e.g., hs37d5) for BWA aligner

fadir Directory

directory containing FastA file and index for BWA aligner

nthreads Integer

The number of cores to be used for parallel exec of fastq-dump

download_repo String (Optional)

(optional) The repository from which the data was downloaded (ncbi/ebi/ddbj). Default value is NCBI.

Steps

ID Runs Label Doc
sam2bam
../Tools/samtools-sam2bam.cwl (CommandLineTool)
samtools-sam2bam-1.9--h8ee4bcc_1
qc2
../Tools/fastqc.cwl (CommandLineTool)
fastqc
qc2P
../Tools/fastqc.cwl (CommandLineTool)
fastqc
qc1P
../Tools/fastqc.cwl (CommandLineTool)
fastqc
pfastq_dump
../Tools/pfastq-dump.cwl (CommandLineTool)
pfastq-dump: A bash implementation of parallel-fastq-dump, parallel fastq-dump wrapper

pfastq-dump is a bash implementation of parallel-fastq-dump, parallel fastq-dump wrapper. --stdout option is additionally supported, but almost same features. It also uses -N and -X options of fastq-dump to specify blocks of data to be decompressed separately. https://github.com/inutano/pfastq-dump

sort
../Tools/samtools-sort.cwl (CommandLineTool)
samtools-sam2bam-1.9--h8ee4bcc_1
download_sra
../Tools/download-sra.cwl (CommandLineTool)
download-sra: A simple download tool to get .sra file

A simple download tool to get .sra file from a repository of INSDC members. https://github.com/inutano/download-sra

map
../Tools/bwa-mem-PE.cwl (CommandLineTool)
bwa-mem-PE-0.7.15--1
qc1
../Tools/fastqc.cwl (CommandLineTool)
fastqc
trimPE
../Tools/trimmomaticPE.cwl (CommandLineTool)
trimmomatic-0.38

Outputs

ID Type Label Doc
oqc1P File
oqc1 File
oqc2 File
sam File
oqc2P File
osort File
bam File
Permalink: https://w3id.org/cwl/view/git/81f0de7c39c54830ce7ed3dec8d747b9a05bb09e/Workflows/test-workflow-from-SRA-Run-id.cwl