SraDownload#

Add to module run order:
#BioModule biolockj.module.getData.sra.SraDownload

Description#

SraDownload downloads and compresses short read archive (SRA) files to fastq.gz

Properties#

Properties are the name=value pairs in the configuration file.

SraDownload properties:#

Property Description
exe.fasterq-dump executable
Path for the "fasterq-dump" executable; if not supplied, any script that needs the fasterq-dump command will assume it is on the PATH.
default: null
sra.accessionIdColumn string
Specifies the metadata file column name containing SRA run ids
default: null
sra.destinationDir file path
Path to directory where downloaded files should be saved. If specified, it must exist.
default: null
sra.sraAccList file path
A file that has one SRA accession per line and nothing else.
default: null
sra.sraProjectId list
The project id(s) referencesing a project in the NCBI SRA. example: SRP009633, ERP016051
default: null

General properties applicable to this module:#

Property Description
cluster.batchCommand string
Terminal command used to submit jobs on the cluster
default: null
cluster.jobHeader string
Header written at top of worker scripts
default: null
cluster.modules list
List of cluster modules to load at start of worker scripts
default: null
cluster.prologue string
To run at the start of every script after loading cluster modules (if any)
default: null
cluster.statusCommand string
Terminal command used to check the status of jobs on the cluster
default: null
docker.saveContainerOnExit boolean
If Y, docker run command will NOT include the --rm flag
default: null
docker.verifyImage boolean
In check dependencies, run a test to verify the docker image.
default: null
exe.gzip executable
Path for the "gzip" executable; if not supplied, any script that needs the gzip command will assume it is on the PATH.
default: null
metadata.filePath file path
If absolute file path, use file as metadata.
If directory path, must find exactly 1 file within, to use as metadata.
default: null
script.defaultHeader string
Store default script header for MAIN script and locally run WORKER scripts.
default: #!/bin/bash
script.numThreads integer
Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.
default: 8
script.numWorkers integer
Set number of samples to process per script (if parallel processing)
default: 1
script.permissions string
Used as chmod permission parameter (ex: 774)
default: 770
script.timeout integer
Sets # of minutes before worker scripts times out.
default: null

Details#

version: 1.0.0 Downloading and compressing files requires fasterq-dump and gzip.The accessions to download can be specified using any ONE of the following:
1. A metadata file (given by metadata.filePath that has column sra.accessionIdColumn.
2. sra.sraProjectId, OR
3. sra.sraAccList
sra.destinationDir gives an external directory that can be shared across pipelines. This is recommended. If it is not specified, the files will be downlaoded to this modules output directory.
Suggested: input.dirPaths = ${sra.destinationDir}
Typically, BioLockJ will automatically determine modules to add to the pipeline to process sequence data. If the files are not present on the system when the pipeline starts, then it is up to the user to configure any and all sequence processing modules.

Adds modules#

pre-requisite modules
none found
post-requisite modules
none found

Docker#

If running in docker, this module will run in a docker container from this image:

biolockjdevteam/sratoolkit:v1.3.18

This can be modified using the following properties:
SraDownload.imageOwner
SraDownload.imageName
SraDownload.imageTag

Citation#

sra-tools
Module developed by Philip Badzuh.