API and CLI reference

BALSAMIC

BALSAMIC 4.2.0: Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer

BALSAMIC [OPTIONS] COMMAND [ARGS]...

Options

--loglevel <loglevel>

Set the level of log output. [default: DEBUG]

Options:DEBUG|INFO|WARNING|ERROR|CRITICAL
--version

Show the version and exit.

config

create config files required for running the pipeline.

BALSAMIC config [OPTIONS] COMMAND [ARGS]...

case

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.

BALSAMIC config case [OPTIONS]

Options

--umi, --no-umi

UMI processing steps for samples with umi tags [default: True]

--umi-trim-length <umi_trim_length>

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 <reference_config>

Reference config file. [required]

-p, --panel-bed <panel_bed>

Panel bed file for variant calling.

-o, --output-config <output_config>

Output a json config filename ready to be imported for run-analysis

-t, --tumor <tumor>

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 <normal>

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 <case_id>

Sample id that is used for reporting, naming the analysis jobs, and analysis path [required]

--fastq-prefix <fastq_prefix>

Prefix to fastq file. The string that comes after readprefix

--analysis-dir <analysis_dir>

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 <singularity>

Download singularity image for BALSAMIC [required]

reference

Configure workflow for reference generation

BALSAMIC config reference [OPTIONS]

Options

-o, --outdir <outdir>

output directory for ref files eg: reference [required]

-c, --cosmic-key <cosmic_key>

cosmic db authentication key [required]

-s, --snakefile <snakefile>

snakefile for reference generation [default: /home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v4.2.0/BALSAMIC/workflows/GenerateRef]

-d, --dagfile <dagfile>

DAG file for overview [default: generate_ref_worflow_graph]

--singularity <singularity>

Download singularity image for BALSAMIC [required]

plugins

Additional and helper utilities for third party applications

BALSAMIC plugins [OPTIONS] COMMAND [ARGS]...

scout

Create a scout config.yaml file

BALSAMIC plugins scout [OPTIONS]

Options

--sample-config <sample_config>

Sample config file. Output of balsamic config sample [required]

--snv-vcf <snv_vcf>

variant caller to load as vcf_cancer

--tumor <tumor>

sample name for tumor sample

--normal <normal>

sample name for normal sample

--sv-vcf <sv_vcf>

variant caller to load as vcf_cancer_sv

--customer-id <customer_id>

customer id for scout config [required]

target-cov-plot

cli for coverage plot sub-command. Creates coverage plots in result_directory.

BALSAMIC plugins target-cov-plot [OPTIONS]

report

Various command to create report, check status, and prepare delivery files

BALSAMIC report [OPTIONS] COMMAND [ARGS]...

deliver

cli for deliver sub-command. Writes <case_id>.hk in result_directory.

BALSAMIC report deliver [OPTIONS]

Options

--sample-config <sample_config>

Sample config file. Output of balsamic config sample [required]

status

cli for status sub-command.

BALSAMIC report status [OPTIONS]

Options

-s, --sample-config <sample_config>

Sample config file. Output of balsamic config sample [required]

-m, --show-only-missing

Only show missing files. [default: False]

-p, --print-files

Print list of files. Otherwise only final count will be printed. [default: False]

run

Run BALSAMIC on a provided config file

BALSAMIC run [OPTIONS] COMMAND [ARGS]...

analysis

Runs BALSAMIC workflow on the provided sample’s config file

BALSAMIC run analysis [OPTIONS]

Options

-a, --analysis-type <analysis_type>

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.

Options:qc|paired|single
-S, --snake-file <snake_file>

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 <sample_config>

Sample json config file. [required]

--run-mode <run_mode>

Run mode to use. By default SLURM will be used to run the analysis. But local runner also available for local computing [default: cluster]

Options:local|cluster
-c, --cluster-config <cluster_config>

cluster config json file. (eg- SLURM, QSUB) [default: /home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v4.2.0/BALSAMIC/config/cluster.json]

-l, --log-file <log_file>

Log file output for BALSAMIC. This is raw log output from snakemake.

-p, --profile <profile>

cluster profile to submit jobs

Options:slurm|qsub
-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 <qos>

QOS for sbatch jobs. Passed to /home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v4.2.0/BALSAMIC/commands/run/scheduler.py [default: low]

Options:low|normal|high
-f, --force-all

Force run all analysis. This is same as snakemake –forceall [default: False]

--snakemake-opt <snakemake_opt>

Pass these options directly to snakemake

--account, --slurm-account, --qsub-account <account>

cluster account to run jobs, ie: slurm_account

--mail-user <mail_user>

cluster mail user to send out email. e.g.: slurm_mail_user

--mail-type <mail_type>

cluster mail type to send out email. This will be applied to all jobs and override snakemake settings.

Options:NONE|BEGIN|END|FAIL|REQUEUE|ALL|TIME_LIMIT

reference

Run generate reference workflow

BALSAMIC run reference [OPTIONS]

Options

-s, --snakefile <snakefile>

snakefile for reference generation

-c, --configfile <configfile>

Config file to run the workflow [required]

--run-mode <run_mode>

Run mode to use. Only local supported for this.

Options:local
--cluster-config <cluster_config>

SLURM config json file. [default: /home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v4.2.0/BALSAMIC/config/cluster.json]

-l, --log-file <log_file>

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]

-f, --force-all

Force run all analysis. This is same as snakemake –forceall [default: False]

--snakemake-opt <snakemake_opt>

Pass these options directly to snakemake