Documentation

README.md

@@ -8,5 +8,75 @@ takes use of other CLI apps in the Clinical-Genomics suite, [hosekeeper](https:/
 and [scout](https://github.com/Clinical-Genomics/scout), to assemble all relevant files, and meta-data about a case as
 input to MutAcc.  
 
-##Install
+## Dependencies
 
+mutacc-auto depends on housekeeper >= 2.2 and scout >= 4.2. These tools must be installed first. mutacc-auto also uses the slurm workload manager to submit jobs.  
+
+## Install
+
+mutacc-auto can be installed using pip,
+
+```console
+git clone https://github.com/Clinical-Genomics/mutacc-auto.git
+cd mutacc-auto
+pip install -e .
+```
+## Usage
+
+### Extract
+
+To use mutacc extract feature on a given case the 'extract' subcommand is used
+
+To extract the clinically relevant reads from a case used
+
+```console
+mutacc-auto extract \
+--config-file <mutacc_configuration> \
+--case-id <case_id> \
+--environment <conda_env> \
+```
+
+slurm specific options can be given with options --log-directory, --email.
+
+full list of options
+
+```console
+Usage: mutacc-auto extract [OPTIONS]
+
+Options:
+  -c, --case-id TEXT        case id used in scout and housekeeper
+  -d, --days-ago INTEGER    days since last update of case
+  -e, --environment TEXT    conda environment used for mutacc
+  -C, --config-file PATH    configuration file used for mutacc
+  -L, --log-directory PATH  Directory for slurm logs
+  -E, --email TEXT          email to notify
+  -p, --padding INTEGER     padding for genomic regions. this defaults to 0
+                            for WES cases
+  -D, --dry                 dry run
+  -V, --verbose             verbose
+  -k, --conda               Use 'conda activate' to source environment
+  --help                    Show this message and exit.
+
+```
+
+### Import
+
+To import the extracted cases into the database (specified in the mutacc configuration file) the
+'import' subcommand is used.
+
+```console
+mutacc-auto import \
+--config-file <mutacc_configuration> 
+```
+
+This will import all extracted cases.
+
+```console
+Usage: mutacc-auto import [OPTIONS]
+
+Options:
+  -C, --config-file PATH  configuration file used for mutacc
+  -D, --dry               dry run
+  -V, --verbose           verbose
+  --help                  Show this message and exit.
+```

mutacc_auto/cli/extract_command.py

@@ -13,16 +13,38 @@
 LOG = logging.getLogger(__name__)
 
 @click.command('extract')
-@click.option('-c','--case-id', type=str)
-@click.option('-d','--days-ago', type=int)
-@click.option('-e','--environment', type=str)
-@click.option('-C','--config-file', type=click.Path(exists=True))
-@click.option('-L', '--log-directory', type=click.Path(exists=True))
-@click.option('-E', '--email', type=str)
-@click.option('-p','--padding', type=int)
-@click.option('-D','--dry', is_flag=True)
-@click.option('-V','--verbose', is_flag=True)
-@click.option('-k', '--conda', is_flag=True)
+@click.option('-c','--case-id',
+type=str,
+help="case id used in scout and housekeeper")
+@click.option('-d','--days-ago',
+type=int,
+help="days since last update of case")
+@click.option('-e','--environment',
+type=str,
+help="conda environment used for mutacc"
+)
+@click.option('-C','--config-file',
+type=click.Path(exists=True),
+help="configuration file used for mutacc"
+)
+@click.option('-L', '--log-directory',
+type=click.Path(exists=True),
+help="Directory for slurm logs")
+@click.option('-E', '--email',
+type=str,
+help="email to notify")
+@click.option('-p','--padding',
+type=int,
+help="padding for genomic regions. this defaults to 0 for WES cases")
+@click.option('-D','--dry',
+is_flag=True,
+help="dry run")
+@click.option('-V','--verbose',
+is_flag=True,
+help="verbose")
+@click.option('-k', '--conda',
+is_flag=True,
+help="Use 'conda activate' to source environment")
 @click.pass_context
 def extract_command(ctx,
                     case_id,

mutacc_auto/cli/import_command.py

@@ -14,9 +14,15 @@
 LOG = logging.getLogger(__name__)
 
 @click.command('import')
-@click.option('-C','--config-file', type=click.Path(exists=True))
-@click.option('-D','--dry', is_flag=True)
-@click.option('-V','--verbose', is_flag=True)
+@click.option('-C','--config-file',
+type=click.Path(exists=True),
+help="configuration file used for mutacc")
+@click.option('-D','--dry',
+is_flag=True,
+help="dry run")
+@click.option('-V','--verbose',
+is_flag=True,
+help="verbose")
 @click.pass_context
 def import_command(ctx,
                    config_file,