# ggr-cwl-ipynb-gen
Jupyter notebook generator to download and execute the processing files for GGR related datasets.
At this point, is not intented to cover all use cases, but to serve as a quick generator of all
related files and scripts to pre-process genomic data generated at the [Duke-GCB Sequencing Core](https://genome.duke.edu/cores-and-services/sequencing-and-genomic-technologies) in [HARDAC](https://genome.duke.edu/cores-and-services/computational-solutions/compute-environments-genomics).
Example of usage:
```
$ ggr_cwl_ipynb_gen \
--root-dir /path/to/rootdir \
--metadata examples/Hong_3979_170316B1.xlsx \
--out /path/to/output_dir \
--force
```
The information in the example metadata and configuration file should reveal what is needed to download and pre-process the samples.
For a full list of options:
```
$ 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)
--project-name PROJECT_NAME
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:
${USER}@duke.edu)
-r ROOT_DIR, --root-dir ROOT_DIR
Root directory where all subfolders and files will be
created (semi-required: either defined here or in
conf-file)
-v VERSION, --version VERSION
Print version of the program and exit
```
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"description": "# ggr-cwl-ipynb-gen\nJupyter notebook generator to download and execute the processing files for GGR related datasets.\nAt this point, is not intented to cover all use cases, but to serve as a quick generator of all\nrelated files and scripts to pre-process genomic data generated at the [Duke-GCB Sequencing Core](https://genome.duke.edu/cores-and-services/sequencing-and-genomic-technologies) in [HARDAC](https://genome.duke.edu/cores-and-services/computational-solutions/compute-environments-genomics).\n\nExample of usage:\n```\n$ ggr_cwl_ipynb_gen \\\n --root-dir /path/to/rootdir \\\n --metadata examples/Hong_3979_170316B1.xlsx \\\n --out /path/to/output_dir \\\n --force\n```\nThe information in the example metadata and configuration file should reveal what is needed to download and pre-process the samples.\n\nFor a full list of options:\n```\n$ ggr_cwl_ipynb_gen -h\nusage: Generator of Jupyter notebooks to execute CWL pre-processing pipelines\n [-h] -o OUT -m METADATA [-f] [-n] [--metadata-sep SEP]\n [--project-name PROJECT_NAME]\n [--data-from {dukeds,sftp,miseq,other,local}] [-c CONF_FILE] [-u USER]\n [-e USER_DUKE_EMAIL] [-r ROOT_DIR] [-v VERSION]\n\noptional arguments:\n -h, --help show this help message and exit\n -o OUT, --out OUT Jupyter notebook output file name\n -m METADATA, --metadata METADATA\n Metadata file with samples information\n -f, --force Force to overwrite output file\n -n, --no-upload Avoids uploading generated data to database when\n specified\n --metadata-sep SEP Separator for metadata file (when different than Excel\n spread sheet)\n --project-name PROJECT_NAME\n Project name (by default, basename of metadata file\n name)\n --data-from {dukeds,sftp,miseq,other,local}\n Choices: dukeds, sftp, miseq, other, local\n -c CONF_FILE, --conf-file CONF_FILE\n YAML configuration file (see examples)\n -u USER, --user USER HARDAC User used in SLURM (default: ${USER})\n -e USER_DUKE_EMAIL, --user-duke-email USER_DUKE_EMAIL\n Email(s) notified when execution is finished (default:\n ${USER}@duke.edu)\n -r ROOT_DIR, --root-dir ROOT_DIR\n Root directory where all subfolders and files will be\n created (semi-required: either defined here or in\n conf-file)\n -v VERSION, --version VERSION\n Print version of the program and exit\n```\n",
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