geofetch usage reference
geofetch command-line usage instructions:
geofetch --help
usage: geofetch [<args>]
The example how to use geofetch (to download GSE573030 just metadata): geofetch -i GSE67303 -m <folder> --just-metadata
To download all processed data of GSE57303: geofetch -i GSE67303 --processed --geo-folder <folder> -m <folder>
Automatic GEO and SRA data downloader
options: -h, --help show this help message and exit -V, --version show program's version number and exit -i INPUT, --input INPUT required: a GEO (GSE) accession, or a file with a list of GSE numbers -n NAME, --name NAME Specify a project name. Defaults to GSE number -m METADATA_ROOT, --metadata-root METADATA_ROOT Specify a parent folder location to store metadata. The project name will be added as a subfolder [Default: $SRAMETA:] -u METADATA_FOLDER, --metadata-folder METADATA_FOLDER Specify an absolute folder location to store metadata. No subfolder will be added. Overrides value of --metadata-root. --just-metadata If set, don't actually run downloads, just create metadata -r, --refresh-metadata If set, re-download metadata even if it exists. --config-template CONFIG_TEMPLATE Project config yaml file template. --pipeline-samples PIPELINE_SAMPLES Optional: Specify one or more filepaths to SAMPLES pipeline interface yaml files. These will be added to the project config file to make it immediately compatible with looper. [Default: null] --pipeline-project PIPELINE_PROJECT Optional: Specify one or more filepaths to PROJECT pipeline interface yaml files. These will be added to the project config file to make it immediately compatible with looper. [Default: null] --disable-progressbar Optional: Disable progressbar -k SKIP, --skip SKIP Skip some accessions. [Default: no skip]. --acc-anno Optional: Produce annotation sheets for each accession. Project combined PEP for the whole project won't be produced. --discard-soft Optional: After creation of PEP files, all .soft files will be deleted --const-limit-project CONST_LIMIT_PROJECT Optional: Limit of the number of the constant sample characters that should not be in project yaml. [Default: 50] --const-limit-discard CONST_LIMIT_DISCARD Optional: Limit of the number of the constant sample characters that should not be discarded [Default: 250] --attr-limit-truncate ATTR_LIMIT_TRUNCATE Optional: Limit of the number of sample characters.Any attribute with more than X characters will truncate to the first X, where X is a number of characters [Default: 500] --add-dotfile Optional: Add .pep.yaml file that points .yaml PEP file --max-soft-size MAX_SOFT_SIZE Optional: Max size of soft file. [Default: 1GB]. Supported input formats : 12B, 12KB, 12MB, 12GB. --max-prefetch-size MAX_PREFETCH_SIZE Argument to pass to prefetch program's --max-size option, if prefetch will be used in this run of geofetch; for reference: https://github.com/ncbi/sra- tools/wiki/08.-prefetch-and-fasterq-dump#check-the- maximum-size-limit-of-the-prefetch-tool --silent Silence logging. Overrides verbosity. --verbosity V Set logging level (1-5 or logging module level name) --logdev Expand content of logging message format.
processed: -p, --processed Download processed data [Default: download raw data]. --data-source {all,samples,series} Optional: Specifies the source of data on the GEO record to retrieve processed data, which may be attached to the collective series entity, or to individual samples. Allowable values are: samples, series or both (all). Ignored unless 'processed' flag is set. [Default: samples] --filter FILTER Optional: Filter regex for processed filenames [Default: None].Ignored unless 'processed' flag is set. --filter-size FILTER_SIZE Optional: Filter size for processed files that are stored as sample repository [Default: None]. Works only for sample data. Supported input formats : 12B, 12KB, 12MB, 12GB. Ignored unless 'processed' flag is set. -g GEO_FOLDER, --geo-folder GEO_FOLDER Optional: Specify a location to store processed GEO files. Ignored unless 'processed' flag is set.[Default: $GEODATA:]
raw: -x, --split-experiments Split SRR runs into individual samples. By default, SRX experiments with multiple SRR Runs will have a single entry in the annotation table, with each run as a separate row in the subannotation table. This setting instead treats each run as a separate sample -b BAM_FOLDER, --bam-folder BAM_FOLDER Optional: Specify folder of bam files. Geofetch will not download sra files when corresponding bam files already exist. [Default: $SRABAM:] -f FQ_FOLDER, --fq-folder FQ_FOLDER Optional: Specify folder of fastq files. Geofetch will not download sra files when corresponding fastq files already exist. [Default: $SRAFQ:] --use-key-subset Use just the keys defined in this module when writing out metadata. --add-convert-modifier Add looper SRA convert modifier to config file.