CLI code reference¶
BALSAMIC¶
BALSAMIC 4.5.0: 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¶
Create a sample config file from input sample data
BALSAMIC config case [OPTIONS]
Options
-
--case-id
<case_id>
¶ Sample id that is used for reporting, naming the analysis jobs, and analysis path [required]
-
--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.
-
--singularity
<singularity>
¶ Download singularity image for BALSAMIC [required]
-
--analysis-dir
<analysis_dir>
¶ Root analysis path to store analysis logs and results. The final path will be analysis-dir/sample-id [required]
-
-t
,
--tumor
<tumor>
¶ Fastq files for tumor sample. [required]
-
-n
,
--normal
<normal>
¶ Fastq files for normal sample.
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/v4.5.0/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]
-
-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
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/v4.5.0/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/v4.5.0/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/v4.5.0/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