refactor: Remove plugins

BALSAMIC/commands/base.py

@@ -8,7 +8,6 @@
 from BALSAMIC.commands.config.base import config as config_command
 from BALSAMIC.commands.init.base import initialize as init_command
 from BALSAMIC.commands.options import OPTION_LOG_LEVEL
-from BALSAMIC.commands.plugins.base import plugins as plugins_command
 from BALSAMIC.commands.report.base import report as report_command
 from BALSAMIC.commands.run.base import run as run_command
 from BALSAMIC.constants.constants import LogLevel
@@ -43,5 +42,4 @@ def cli(context: click.Context, log_level: LogLevel):
 cli.add_command(run_command)
 cli.add_command(report_command)
 cli.add_command(config_command)
-cli.add_command(plugins_command)
 cli.add_command(init_command)

BALSAMIC/snakemake_rules/align/sentieon_alignment.rule

@@ -101,7 +101,7 @@ rule sentieon_realign:
         Path(benchmark_dir, "sentieon_realign_{sample_type}.{sample}.tsv").as_posix()
     params:
         tmpdir = tempfile.mkdtemp(prefix=tmp_dir),
-        sentieon_exec = config["SENTIEON_EXEC"],
+         sentieon_exec = config["SENTIEON_EXEC"],
         sentieon_lic = config["SENTIEON_LICENSE"],
         sample_id = "{sample}"
     threads:

CHANGELOG.rst

@@ -59,7 +59,7 @@ Removed:
 * Config folder https://github.com/Clinical-Genomics/BALSAMIC/pull/1175
 * Quality trimming of fastqs for UMI workflow https://github.com/Clinical-Genomics/BALSAMIC/pull/1176
 * Balsamic container https://github.com/Clinical-Genomics/BALSAMIC/pull/1230
-
+* Plugin CLI https://github.com/Clinical-Genomics/BALSAMIC/pull/1245
 
 [12.0.2]
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