p3-submit-fastqutils¶

Submit a Fastq Utilities Job¶

This script submits a Fastqutils job to BV-BRC. It allows input from all supported read libraries, and requests a list of services to be performed.

Usage Synopsis¶

p3-submit-fastqutils [options] output-path output-name

Start a FASTQ processing job specified workspace path, using the specified name for the output job folder.

Command-Line Options¶

–paired-end-lib

Two paired-end libraries containing reads. These are coded with a single invocation, e.g. --paired-end-lib left.fa right.fa. The libraries must be paired FASTQ files. A prefix of ws: indicates a file is in the BV-BRC workspace; otherwise they are uploaded from the local file system. This parameter may be specified multiple times.

=item –single-end-lib

A library of single reads. This must be a FASTQ file. A prefix of ws: indicates a file is in the BV-BRC workspace; otherwise they are uploaded from the local file system. This parameter may be specified multiple times.

–srr-id

A run ID from the NCBI sequence read archive. The run will be downloaded from the NCBI for processing. This parameter may be specified multiple times.

–trim

Trim the sequences. This operation is performed before quality control.

–paired_filter

Perform paired-end filtering. This operation is always performed first.

–fastqc

Run the FASTQ quality control analysis. This operation is performed after trimming.

–reference-genome-id

If specified, the ID of a genome in BV-BRC to which the reads will be aligned. This operation is always performed last.

–workspace-path-prefix

Base workspace directory for relative workspace paths.

–workspace-upload-path

Name of workspace directory to which local files should be uplaoded.

–overwrite

If a file to be uploaded already exists and this parameter is specified, it will be overwritten; otherwise, the script will error out.

–help

Display the command-line usage and exit.

–dry-run

Display the JSON submission string and exit without invoking the service or uploading files.