Feat/ascat download container (#689)

* Add ascat container * changelog * remove ascat * Add ascatngs as submodule * Add ascatngs
Clinical-Genomics · Jul 23, 2021 · 9ed348a · 9ed348a
1 parent 043add2
commit 9ed348a
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Showing 4 changed files with 11 additions and 5 deletions.
diff --git 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
@@ -29,3 +29,5 @@ vcf_merge:
   - vcfmerge
 varcall_delly:
   - delly
+ascatngs:
+  -ascat
diff --git 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
@@ -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:
 ^^^^^^^^