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Update README.md #22

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33 changes: 22 additions & 11 deletions README.md
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Expand Up @@ -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 \
Expand All @@ -15,27 +15,38 @@ 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
-o OUT, --out OUT Jupyter notebook output file name
-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
```