CLI code reference

BALSAMIC

BALSAMIC 6.1.2: 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

Create a sample config file from input sample data

BALSAMIC config case [OPTIONS]

Options

--case-id <case_id>

Required Sample id that is used for reporting, naming the analysis jobs, and analysis path

--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:True
-r, --reference-config <reference_config>

Required Reference config file.

-p, --panel-bed <panel_bed>

Panel bed file for variant calling.

-b, --background-variants <background_variants>

Background set of valid variants for UMI

--singularity <singularity>

Required Download singularity image for BALSAMIC

--analysis-dir <analysis_dir>

Required Root analysis path to store analysis logs and results. The final path will be analysis-dir/sample-id

-t, --tumor <tumor>

Required Fastq files for tumor sample.

-n, --normal <normal>

Fastq files for normal sample.

--tumor-sample-name <tumor_sample_name>

Tumor sample name

--normal-sample-name <normal_sample_name>

Normal sample name

reference

Configure workflow for reference generation

BALSAMIC config reference [OPTIONS]

Options

-o, --outdir <outdir>

Required output directory for ref files eg: reference

-c, --cosmic-key <cosmic_key>

Required cosmic db authentication key

-s, --snakefile <snakefile>

snakefile for reference generation

Default:/home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v6.1.2/BALSAMIC/workflows/GenerateRef
-d, --dagfile <dagfile>

DAG file for overview

Default:generate_ref_worflow_graph
--singularity <singularity>

Required Download singularity image for BALSAMIC

-g, --genome-version <genome_version>

Genome version to prepare reference. Path to genomewill be <outdir>/genome_version

Options:hg19|hg38

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>

Required Sample config file. Output of balsamic config sample

--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>

Required customer id for scout config

target-cov-plot

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

BALSAMIC plugins target-cov-plot [OPTIONS]

vcfutils

Commands to process VCF files

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

Filter input variants from reference VCF

BALSAMIC plugins vcfutils createvcf [OPTIONS]

Options

-i, --input_file <input_file>

Required tab-seperated reference text file

-r, --reference_file <reference_file>

Required cosmic database file

-o, --output_file <output_file>

Required Output file name

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

-s, --sample-config <sample_config>

Required Sample config file. Output of balsamic config sample

--sample-id-map <sample_id_map>

Separated internal sample ID with external ID. Use comma formultiple samples. These IDs MUST exist in sample-config.Syntax: internal_id:sample_type:external_id. e.g. ACC1:tumor:KS454,ACC2:normal:KS556

--case-id-map <case_id_map>

Separated internal case ID with external ID.Syntax: gene_panel_name:external_id. e.g. gmck-solid:KSK899:apptag

-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 fileif it is set here.

Options:qc|paired|single
-r, --rules-to-deliver <rules_to_deliver>

Specify a rule to deliver. Delivery mode selected via –delivery-mode option

-m, --delivery-mode <delivery_mode>

a: append rules-to-deliver to current delivery options. or r: reset current rules to delivery to only the ones specified

Default:a
Options:a|r

status

cli for status sub-command.

BALSAMIC report status [OPTIONS]

Options

-s, --sample-config <sample_config>

Required Sample config file. Output of balsamic config sample

-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:paired|single|umi|qc
-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>

Required Sample json config file.

--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/v6.1.2/BALSAMIC/config/cluster.json
-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/v6.1.2/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
--disable-variant-caller <disable_variant_caller>

Run workflow with selected variant caller disable.

Options:tnsnv|tnscope|tnhaplotyper|dnascope|manta|cnvkit|mutect|vardict|strelka|manta_germline|haplotypecaller|strelka_germline

reference

Run generate reference workflow

BALSAMIC run reference [OPTIONS]

Options

-s, --snakefile <snakefile>

snakefile for reference generation

-c, --configfile <configfile>

Required Config file to run the workflow

--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/v6.1.2/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