diff --git a/BALSAMIC/commands/config/case.py b/BALSAMIC/commands/config/case.py index 34d5d8961..5aa0c7e99 100644 --- a/BALSAMIC/commands/config/case.py +++ b/BALSAMIC/commands/config/case.py @@ -10,7 +10,7 @@ get_bioinfo_tools_version, create_fastq_symlink, generate_graph) from BALSAMIC.utils.constants import (CONTAINERS_CONDA_ENV_PATH, VCF_DICT, - BIOINFO_TOOL_ENV) + BIOINFO_TOOL_ENV, BIOINFO_TOOL_SUBMODULE) from BALSAMIC.utils.models import BalsamicConfigModel LOG = logging.getLogger(__name__) @@ -131,7 +131,7 @@ def case_config(context, case_id, umi, umi_trim_length, adapter_trim, background_variants=background_variants, samples=samples, vcf=VCF_DICT, - bioinfo_tools=BIOINFO_TOOL_ENV, + bioinfo_tools={**BIOINFO_TOOL_ENV, **BIOINFO_TOOL_SUBMODULE}, bioinfo_tools_version=get_bioinfo_tools_version( BIOINFO_TOOL_ENV, CONTAINERS_CONDA_ENV_PATH), panel={ diff --git a/BALSAMIC/config/balsamic_env.yaml b/BALSAMIC/config/balsamic_env.yaml index fb5c2959c..50f5ac6fa 100644 --- a/BALSAMIC/config/balsamic_env.yaml +++ b/BALSAMIC/config/balsamic_env.yaml @@ -29,3 +29,5 @@ vcf_merge: - vcfmerge varcall_delly: - delly +ascatngs: + -ascat diff --git a/BALSAMIC/utils/constants.py b/BALSAMIC/utils/constants.py index 76f347297..1ce727776 100644 --- a/BALSAMIC/utils/constants.py +++ b/BALSAMIC/utils/constants.py @@ -595,7 +595,7 @@ # list of bioinfo tools for each conda env VALID_CONTAINER_CONDA_NAME = { "align_qc", "annotate", "coverage_qc", "varcall_py36", "varcall_py27", - "varcall_cnvkit","varcall_delly" + "varcall_cnvkit","varcall_delly","ascatngs" } BIOINFO_TOOL_ENV = { @@ -619,7 +619,11 @@ "strelka": "varcall_py27", "manta": "varcall_py27", "cnvkit": "varcall_cnvkit", - "delly": "varcall_delly" + "delly": "varcall_delly", +} + +BIOINFO_TOOL_SUBMODULE = { + "ascat": "ascatngs" } REPORT_MODEL = { diff --git a/CHANGELOG.rst b/CHANGELOG.rst index b83e3861b..651176372 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -21,7 +21,7 @@ Added: * Reference section to docs/FAQ.rst * ascat download references from reference_file repository * Delly tumor only rule - +* ascat download container Changed: ^^^^^^^^