Index

Symbols

--account, --slurm-account, --qsub-account <account> BALSAMIC-run-analysis command line option --adapter-trim, --no-adapter-trim BALSAMIC-config-case command line option --analysis-dir <analysis_dir> BALSAMIC-config-case command line option --case-id <case_id> BALSAMIC-config-case command line option --cluster-config <cluster_config> BALSAMIC-run-reference command line option --create-dir, --no-create-dir BALSAMIC-config-case command line option --customer-id <customer_id> BALSAMIC-plugins-scout command line option --fastq-prefix <fastq_prefix> BALSAMIC-config-case command line option --loglevel <loglevel> BALSAMIC command line option --mail-type <mail_type> BALSAMIC-run-analysis command line option --mail-user <mail_user> BALSAMIC-run-analysis command line option --normal <normal> BALSAMIC-plugins-scout command line option --overwrite-config, --no-overwrite-config BALSAMIC-config-case command line option --qos <qos> BALSAMIC-run-analysis command line option --quality-trim, --no-quality-trim BALSAMIC-config-case command line option --run-mode <run_mode> BALSAMIC-run-analysis command line option BALSAMIC-run-reference command line option --sample-config <sample_config> BALSAMIC-plugins-scout command line option BALSAMIC-report-deliver command line option --singularity <singularity> BALSAMIC-config-case command line option BALSAMIC-config-reference command line option --snakemake-opt <snakemake_opt> BALSAMIC-run-analysis command line option BALSAMIC-run-reference command line option --snv-vcf <snv_vcf> BALSAMIC-plugins-scout command line option --sv-vcf <sv_vcf> BALSAMIC-plugins-scout command line option --tumor <tumor> BALSAMIC-plugins-scout command line option --umi, --no-umi BALSAMIC-config-case command line option

--umi-trim-length <umi_trim_length> BALSAMIC-config-case command line option --version BALSAMIC command line option -a, --analysis-type <analysis_type> BALSAMIC-run-analysis command line option -c, --cluster-config <cluster_config> BALSAMIC-run-analysis command line option -c, --configfile <configfile> BALSAMIC-run-reference command line option -c, --cosmic-key <cosmic_key> BALSAMIC-config-reference command line option -d, --dagfile <dagfile> BALSAMIC-config-reference command line option -f, --force-all BALSAMIC-run-analysis command line option BALSAMIC-run-reference command line option -l, --log-file <log_file> BALSAMIC-run-analysis command line option BALSAMIC-run-reference command line option -m, --show-only-missing BALSAMIC-report-status command line option -n, --normal <normal> BALSAMIC-config-case command line option -o, --outdir <outdir> BALSAMIC-config-reference command line option -o, --output-config <output_config> BALSAMIC-config-case command line option -p, --panel-bed <panel_bed> BALSAMIC-config-case command line option -p, --print-files BALSAMIC-report-status command line option -p, --profile <profile> BALSAMIC-run-analysis command line option -r, --reference-config <reference_config> BALSAMIC-config-case command line option -r, --run-analysis BALSAMIC-run-analysis command line option BALSAMIC-run-reference command line option -s, --sample-config <sample_config> BALSAMIC-report-status command line option BALSAMIC-run-analysis command line option -S, --snake-file <snake_file> BALSAMIC-run-analysis command line option -s, --snakefile <snakefile> BALSAMIC-config-reference command line option BALSAMIC-run-reference command line option -t, --tumor <tumor> BALSAMIC-config-case command line option

A

add_doc() (in module BALSAMIC.utils.cli)

B

BALSAMIC (module) BALSAMIC command line option --loglevel <loglevel> --version BALSAMIC-config-case command line option --adapter-trim, --no-adapter-trim --analysis-dir <analysis_dir> --case-id <case_id> --create-dir, --no-create-dir --fastq-prefix <fastq_prefix> --overwrite-config, --no-overwrite-config --quality-trim, --no-quality-trim --singularity <singularity> --umi, --no-umi --umi-trim-length <umi_trim_length> -n, --normal <normal> -o, --output-config <output_config> -p, --panel-bed <panel_bed> -r, --reference-config <reference_config> -t, --tumor <tumor> BALSAMIC-config-reference command line option --singularity <singularity> -c, --cosmic-key <cosmic_key> -d, --dagfile <dagfile> -o, --outdir <outdir> -s, --snakefile <snakefile> BALSAMIC-plugins-scout command line option --customer-id <customer_id> --normal <normal> --sample-config <sample_config> --snv-vcf <snv_vcf> --sv-vcf <sv_vcf> --tumor <tumor> BALSAMIC-report-deliver command line option --sample-config <sample_config> BALSAMIC-report-status command line option -m, --show-only-missing -p, --print-files -s, --sample-config <sample_config> BALSAMIC-run-analysis command line option --account, --slurm-account, --qsub-account <account> --mail-type <mail_type> --mail-user <mail_user> --qos <qos> --run-mode <run_mode> --snakemake-opt <snakemake_opt> -S, --snake-file <snake_file> -a, --analysis-type <analysis_type> -c, --cluster-config <cluster_config> -f, --force-all -l, --log-file <log_file> -p, --profile <profile> -r, --run-analysis -s, --sample-config <sample_config>

BALSAMIC-run-reference command line option --cluster-config <cluster_config> --run-mode <run_mode> --snakemake-opt <snakemake_opt> -c, --configfile <configfile> -f, --force-all -l, --log-file <log_file> -r, --run-analysis -s, --snakefile <snakefile> BALSAMIC.assets (module) BALSAMIC.commands (module) BALSAMIC.commands.base (module) BALSAMIC.commands.config (module) BALSAMIC.commands.config.base (module) BALSAMIC.commands.config.case (module) BALSAMIC.commands.config.reference (module) BALSAMIC.commands.plugins (module) BALSAMIC.commands.plugins.base (module) BALSAMIC.commands.plugins.cov_plot (module) BALSAMIC.commands.plugins.scout (module) BALSAMIC.commands.report (module) BALSAMIC.commands.report.base (module) BALSAMIC.commands.report.deliver (module) BALSAMIC.commands.report.status (module) BALSAMIC.commands.run (module) BALSAMIC.commands.run.analysis (module) BALSAMIC.commands.run.base (module) BALSAMIC.commands.run.reference (module) BALSAMIC.commands.run.scheduler (module) BALSAMIC.utils (module) BALSAMIC.utils.cli (module) BALSAMIC.utils.exc (module) BALSAMIC.utils.rule (module) BalsamicError build_cmd() (BALSAMIC.commands.run.scheduler.QsubScheduler method) (BALSAMIC.commands.run.scheduler.SbatchScheduler method) (BALSAMIC.utils.cli.SnakeMake method)

C

CaptureStdout (class in BALSAMIC.utils.cli) check_exist() (in module BALSAMIC.commands.config.case)

configure_fastq() (in module BALSAMIC.commands.config.case) convert_defaultdict_to_regular_dict() (in module BALSAMIC.utils.cli) createDir() (in module BALSAMIC.utils.cli)

F

find_file_index() (in module BALSAMIC.utils.cli)

G

get_analysis_type() (in module BALSAMIC.commands.config.case) get_chrom() (in module BALSAMIC.utils.rule) get_conda_env() (in module BALSAMIC.utils.rule) get_config() (in module BALSAMIC.utils.cli) get_fastq_path() (in module BALSAMIC.commands.config.case) get_file_extension() (in module BALSAMIC.utils.cli) get_file_status_string() (in module BALSAMIC.utils.cli) get_from_two_key() (in module BALSAMIC.utils.cli) get_output_config() (in module BALSAMIC.commands.config.case) get_package_split() (in module BALSAMIC.utils.cli) get_packages() (in module BALSAMIC.utils.cli)

get_parser() (in module BALSAMIC.commands.run.scheduler) get_picard_mrkdup() (in module BALSAMIC.utils.rule) get_ref_path() (in module BALSAMIC.utils.cli) get_result_dir() (in module BALSAMIC.utils.rule) get_sample_config() (in module BALSAMIC.commands.config.case) get_sample_type() (in module BALSAMIC.utils.rule) get_schedulerpy() (in module BALSAMIC.utils.cli) get_script_path() (in module BALSAMIC.utils.rule) get_snakefile() (in module BALSAMIC.utils.cli) get_threads() (in module BALSAMIC.utils.rule) get_vcf() (in module BALSAMIC.utils.rule)

I

iterdict() (in module BALSAMIC.utils.cli)

L

link_fastq() (in module BALSAMIC.commands.config.case)

M

main() (in module BALSAMIC.commands.run.scheduler)

merge_dict_on_key() (in module BALSAMIC.utils.cli) merge_json() (in module BALSAMIC.commands.config.case)

Q

QsubScheduler (class in BALSAMIC.commands.run.scheduler)

R

read_sample_config() (in module BALSAMIC.commands.run.scheduler)

recursive_default_dict() (in module BALSAMIC.utils.cli)

S

SbatchScheduler (class in BALSAMIC.commands.run.scheduler) set_panel_bed() (in module BALSAMIC.commands.config.case)

SnakeMake (class in BALSAMIC.utils.cli) submit_job() (in module BALSAMIC.commands.run.scheduler)

W

write_json() (in module BALSAMIC.utils.cli)

write_sacct_file() (in module BALSAMIC.commands.run.scheduler)