docker-metaspades

Docker image running metaSPAdes

The purpose of this repository is to build a Docker image running metaSPAdes. It will also contain a wrapper script that will be included within the Docker image that will make it more convenient to run within an HPC (e.g. Slurm) or 'cloud' (e.g. AWS Batch).

Wrapper script options

--input

Specifies the set of FASTQ reads that will be aligned. Supports files from SRA, S3, or FTP. Use the file prefix to specify the source (s3://, sra://, or ftp://). Note that for SRA, users can just provide the accession (e.g. sra://SRR123456).

--output-folder

Folder to place the output in, supporting either s3:// or a local path. Output files will take the form of <prefix>.json.gz, where <prefix> is the SRA accession (if specified), or otherwise the prefix of the input file from S3 or ftp.

--interleaved

Specify TRUE or FALSE to treat the input data as interleaved or not. This is not considered when you provide an SRA accession, as the paired-end nature of the data is guessed automatically.

--threads

Number of threads used by metaSPAdes during assembly, defaults to 16.

--max-mem

Maximum amount of memory to use, in Gb

--overwrite

Overwrite any output data, if present. Default behavior is to skip if a file is present in the output filepath.

--temp-folder

The path to the folder used for temporary space. This should be somewhere with a bit of space for all of the temporary files created by metaSPAdes.