CLI reference¶
BALSAMIC (version = 4.2.1) is using Click. This section covers the CLI reference for BALSAMIC.
Contents
Short summary¶
Base command, balsamic
has three subcommands: 1) install_env
which is used for installting
conda environemnts 2) create_config
is to create a config file
necessary for running the analysis. 3) run_analysis
is for running
the actual workflow.
Base command¶
Usage: balsamic [OPTIONS] COMMAND [ARGS]...
BALSAMIC 4.2.1: Bioinformatic Analysis pipeLine for SomAtic MutatIons in
Cancer
Options:
--loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]
Set the level of log output. [default:
DEBUG]
--version Show the version and exit.
--help Show this message and exit.
Commands:
config create config files required for running the pipeline.
plugins Additional and helper utilities for third party applications
run Run BALSAMIC on a provided config file
create config for case analysis¶
Usage: balsamic config [OPTIONS] COMMAND [ARGS]...
create config files required for running the pipeline.
Options:
--help Show this message and exit.
Commands:
case Create a sample config file from input sample data
reference config workflow for generate reference
Usage: balsamic config case [OPTIONS]
Prepares a config file for balsamic run_analysis. For now it is just
treating json as dictionary and merging them as it is. So this is just a
placeholder for future.
Options:
--umi / --no-umi UMI processing steps for samples with umi
tags [default: True]
--umi-trim-length INTEGER Trim N bases from reads in fastq [default:
5]
--quality-trim / --no-quality-trim
Trim low quality reads in fastq [default:
True]
--adapter-trim / --no-adapter-trim
Trim adapters from reads in fastq [default:
False]
-r, --reference-config PATH Reference config file. [required]
-p, --panel-bed PATH Panel bed file for variant calling.
-o, --output-config TEXT Output a json config filename ready to be
imported for run-analysis
-t, --tumor TEXT Fastq files for tumor sample.
Example: if files are
tumor_fqreads_1.fastq.gz
tumor_fqreads_2.fastq.gz, the
input should be --tumor tumor_fqreads
[required]
-n, --normal TEXT Fastq files for normal sample.
Example: if files are
normal_fqreads_1.fastq.gz
normal_fqreads_2.fastq.gz, the
input should be --normal normal_fqreads
--case-id TEXT Sample id that is used for reporting,
naming the analysis jobs, and analysis path
[required]
--fastq-prefix TEXT Prefix to fastq file. The
string that comes after readprefix
--analysis-dir PATH Root analysis path to store
analysis logs and results. The final path
will be analysis-dir/sample-id
--overwrite-config / --no-overwrite-config
Overwrite output config file
--create-dir / --no-create-dir Create analysis directiry.
--singularity PATH Download singularity image for BALSAMIC
[required]
--help Show this message and exit.
Usage: balsamic config reference [OPTIONS]
Configure workflow for reference generation
Options:
-o, --outdir TEXT output directory for ref files eg: reference
[required]
-c, --cosmic-key TEXT cosmic db authentication key [required]
-s, --snakefile PATH snakefile for reference generation [default: /home/h
assan.foroughi/repos/BALSAMIC/BALSAMIC/workflows/Gene
rateRef]
-d, --dagfile TEXT DAG file for overview [default:
generate_ref_worflow_graph]
--singularity PATH Download singularity image for BALSAMIC [required]
--help Show this message and exit.
run case analysis and reference creation¶
Usage: balsamic run [OPTIONS] COMMAND [ARGS]...
Run BALSAMIC on a provided config file
Options:
--help Show this message and exit.
Commands:
analysis Run the analysis on a provided sample config-file
reference Run the GenerateRef workflow
Usage: balsamic run analysis [OPTIONS]
Runs BALSAMIC workflow on the provided sample's config file
Options:
-a, --analysis-type [qc|paired|single]
Type of analysis to run from input config
file. By default it will read
from config file, but it will override
config file if it is set here.
-S, --snake-file PATH Input for a custom snakefile. WARNING: This
is for internal testing, and
should not be used. Providing a snakefile
supersedes analysis_type option.
-s, --sample-config PATH Sample json config file. [required]
--run-mode [local|slurm] Run mode to use. By default SLURM will be
used to run the analysis. But
local runner also available for local
computing [default: slurm]
-c, --cluster-config PATH SLURM config json file. [default: /home/has
san.foroughi/repos/BALSAMIC/BALSAMIC/config/
cluster.json]
-l, --log-file PATH Log file output for BALSAMIC.
This is raw log output from snakemake.
-r, --run-analysis By default balsamic run_analysis will run in
dry run mode. Raise thise flag
to make the actual analysis [default:
False]
--qos [low|normal|high] QOS for sbatch jobs. Passed to /home/hassan.
foroughi/repos/BALSAMIC/BALSAMIC/commands/ru
n/sbatch.py [default: low]
-f, --force-all Force run all analysis. This is same as
snakemake --forceall [default: False]
--snakemake-opt TEXT Pass these options directly to snakemake
--slurm-account TEXT SLURM account to run jobs
--slurm-mail-user TEXT SLURM mail user to send out email.
--slurm-mail-type [NONE|BEGIN|END|FAIL|REQUEUE|ALL|TIME_LIMIT]
SLURM mail type to send out email.
This will be applied to all jobs and
override snakemake settings.
--help Show this message and exit.
Usage: balsamic run reference [OPTIONS]
Run generate reference workflow
Options:
-s, --snakefile TEXT snakefile for reference generation
-c, --configfile TEXT Config file to run the workflow [required]
--run-mode [slurm|local] Run mode to use.(LOCAL, SLURM for HPC)
--cluster-config PATH SLURM config json file. [default: /home/hassan.fo
roughi/repos/BALSAMIC/BALSAMIC/config/cluster.json
]
-l, --log-file PATH Log file output for BALSAMIC. This is raw log
output from snakemake.
-r, --run-analysis By default balsamic run_analysis will run in dry
run mode. Raise thise flag to make
the actual analysis [default: False]
--qos [low|normal|high] QOS for sbatch jobs. Passed to /home/hassan.foroug
hi/repos/BALSAMIC/BALSAMIC/commands/run/sbatch.py
[default: low]
-f, --force-all Force run all analysis. This is same as snakemake
--forceall [default: False]
--snakemake-opt TEXT Pass these options directly to snakemake
--help Show this message and exit.