diff --git a/README.md b/README.md index ad2c98d..f4dbe95 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ related files and scripts to pre-process genomic data generated at the [Duke-GCB Example of usage: ``` -$ python ggr_cwl_ipynb_gen.py \ +$ ggr_cwl_ipynb_gen \ --root-dir /path/to/rootdir \ --metadata examples/Hong_3979_170316B1.xlsx \ --out /path/to/output_dir \ @@ -15,9 +15,12 @@ The information in the example metadata and configuration file should reveal wha For a full list of options: ``` -$ python ggr_cwl_ipynb_gen.py -h -usage: Generator of Jupyter notebooks to execute CWL pre-processing pipelines [-h] -o OUT -m METADATA [-f] [-n] [--metadata-sep SEP] [--project-name PROJECT_NAME] - [--data-from {sftp,miseq,other,dukeds,local}] [-c CONF_FILE] [-u USER] [-e USER_DUKE_EMAIL] [-r ROOT_DIR] +$ ggr_cwl_ipynb_gen -h +usage: Generator of Jupyter notebooks to execute CWL pre-processing pipelines + [-h] -o OUT -m METADATA [-f] [-n] [--metadata-sep SEP] + [--project-name PROJECT_NAME] + [--data-from {dukeds,sftp,miseq,other,local}] [-c CONF_FILE] [-u USER] + [-e USER_DUKE_EMAIL] [-r ROOT_DIR] [-v VERSION] optional arguments: -h, --help show this help message and exit @@ -25,17 +28,25 @@ optional arguments: -m METADATA, --metadata METADATA Metadata file with samples information -f, --force Force to overwrite output file - -n, --no-upload Avoids uploading generated data to database when specified - --metadata-sep SEP Separator for metadata file (when different than Excel spread sheet) + -n, --no-upload Avoids uploading generated data to database when + specified + --metadata-sep SEP Separator for metadata file (when different than Excel + spread sheet) --project-name PROJECT_NAME - Project name (by default, basename of metadata file name) - --data-from {sftp,miseq,other,dukeds,local} - Choices: sftp, miseq, other, dukeds, local + Project name (by default, basename of metadata file + name) + --data-from {dukeds,sftp,miseq,other,local} + Choices: dukeds, sftp, miseq, other, local -c CONF_FILE, --conf-file CONF_FILE YAML configuration file (see examples) -u USER, --user USER HARDAC User used in SLURM (default: ${USER}) -e USER_DUKE_EMAIL, --user-duke-email USER_DUKE_EMAIL - Email(s) notified when execution is finished (default: ${USER}@duke.edu) + Email(s) notified when execution is finished (default: + ${USER}@duke.edu) -r ROOT_DIR, --root-dir ROOT_DIR - Root directory where all subfolders and files will be created (semi-required: either defined here or in conf-file) + Root directory where all subfolders and files will be + created (semi-required: either defined here or in + conf-file) + -v VERSION, --version VERSION + Print version of the program and exit ```