p3-submit-metagenomic-read-mapping¶
Submit a Metagenomic Read Mapping Job¶
This script submits a Metagenomic Read-Mapping job to BV-BRC. It takes input from read libraries and uses either the CARD or VFDB database to identify the nature of the incoming reads.
Usage Synopsis¶
p3-submit-metagenomic-read-mapping [options] output-path output-name
Start a metagenomic read mapping, producing output in the specified workspace path, using the specified name for the base filename of the output files.
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 ofws:
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.
–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.
–gene-set-name
The gene set name–
CARD
orVFDB
. The default isCARD
.
–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.