refactor: Remove Balsamic container (#1220)

Clinical-Genomics · Aug 10, 2023 · f76d8a1 · f76d8a1
1 parent 99fe9f2
commit f76d8a1
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Showing 14 changed files with 5 additions and 57 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -6,8 +6,6 @@ tag_name = v{new_version}
 
 [bumpversion:file:CITATION.cff]
 
-[bumpversion:file:BALSAMIC/containers/balsamic/Dockerfile]
-
 [bumpversion:file:BALSAMIC/__version__.py]
 
 [bumpversion:file:BALSAMIC/__init__.py]

diff --git a/.github/workflows/docker_build_push.yml b/.github/workflows/docker_build_push.yml
@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
+        container-name: [align_qc, annotate, ascatNgs, cnvpytor, coverage_qc, delly, somalier, varcall_cnvkit, varcall_py3, varcall_py27, vcf2cytosure]
     steps:
       - name: Git checkout
         id: git_checkout

diff --git a/.github/workflows/docker_build_push_release.yml b/.github/workflows/docker_build_push_release.yml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
+        container-name: [align_qc, annotate, ascatNgs, cnvpytor, coverage_qc, delly, somalier, varcall_cnvkit, varcall_py3, varcall_py27, vcf2cytosure]
     steps:
       - name: Git checkout
         id: git_checkout

diff --git a/.github/workflows/docker_build_test_pull_request.yml b/.github/workflows/docker_build_test_pull_request.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
+        container-name: [align_qc, annotate, ascatNgs, cnvpytor, coverage_qc, delly, somalier, varcall_cnvkit, varcall_py3, varcall_py27, vcf2cytosure]
     steps:
       - name: Git checkout
         id: git_checkout

diff --git a/BALSAMIC/constants/cache.py b/BALSAMIC/constants/cache.py
@@ -42,7 +42,6 @@ class DockerContainers(StrEnum):
     ALIGN_QC: str = "align_qc"
     ANNOTATE: str = "annotate"
     ASCAT: str = "ascatNgs"
-    BALSAMIC: str = "balsamic"
     CNVKIT: str = "varcall_cnvkit"
     CNVPYTOR: str = "cnvpytor"
     COVERAGE_QC: str = "coverage_qc"

diff --git a/BALSAMIC/containers/balsamic/Dockerfile b/BALSAMIC/containers/balsamic/Dockerfile
diff --git a/BALSAMIC/containers/balsamic/__init__.py b/BALSAMIC/containers/balsamic/__init__.py
diff --git a/BALSAMIC/containers/balsamic/balsamic.sh b/BALSAMIC/containers/balsamic/balsamic.sh
diff --git a/BALSAMIC/containers/balsamic/balsamic.yaml b/BALSAMIC/containers/balsamic/balsamic.yaml
diff --git a/BALSAMIC/snakemake_rules/concatenation/concatenation.rule b/BALSAMIC/snakemake_rules/concatenation/concatenation.rule
@@ -7,8 +7,6 @@ rule concatenate:
         fastq = concat_dir + "{sample}_R_{read}.fastq.gz"
     benchmark:
         Path(benchmark_dir, "{sample}_R_{read}.tsv").as_posix()
-    singularity:
-        Path(singularity_image, "balsamic.sif").as_posix()
     params:
         fastq_dir = fastq_dir,
         concat_dir = concat_dir,

diff --git a/BALSAMIC/snakemake_rules/quality_control/qc_metrics.rule b/BALSAMIC/snakemake_rules/quality_control/qc_metrics.rule
@@ -24,8 +24,6 @@ rule collect_custom_qc_metrics:
         config_path = analysis_dir + config["analysis"]["case_id"] + ".json",
         collect_qc_metrics_script = get_script_path("collect_qc_metrics.py"),
         housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "qc-metrics"}
-    singularity:
-        Path(singularity_image, "balsamic.sif").as_posix()
     threads:
         get_threads(cluster_config, "collect_custom_qc_metrics")
     message:

diff --git a/BALSAMIC/snakemake_rules/quality_control/report.rule b/BALSAMIC/snakemake_rules/quality_control/report.rule
@@ -9,8 +9,6 @@ rule cnv_report:
     params:
         housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"},
         cnv_report_script= get_script_path("generate_cnv_report.py"),
-    singularity:
-        Path(singularity_image, "balsamic.sif").as_posix()
     threads:
         get_threads(cluster_config, "cnv_report")
     message:

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,5 +1,6 @@
 [X.X.X]
 -------
+
 Added:
 ^^^^^^
 * Fastq concatenation https://github.com/Clinical-Genomics/BALSAMIC/pull/1069
@@ -35,6 +36,7 @@ Fixed:
 Removed:
 ^^^^^^^
 * Config folder https://github.com/Clinical-Genomics/BALSAMIC/pull/1175
+* Balsamic container https://github.com/Clinical-Genomics/BALSAMIC/pull/1220
 
 [12.0.2]
 --------

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -936,7 +936,6 @@ def fixture_develop_containers() -> Dict[str, str]:
         DockerContainers.ASCAT.value: "docker://clinicalgenomics/balsamic:develop-ascatNgs",
         DockerContainers.VCF2CYTOSURE.value: "docker://clinicalgenomics/balsamic:develop-vcf2cytosure",
         DockerContainers.PYTHON_3.value: "docker://clinicalgenomics/balsamic:develop-varcall_py3",
-        DockerContainers.BALSAMIC.value: "docker://clinicalgenomics/balsamic:develop-balsamic",
         DockerContainers.SOMALIER.value: "docker://clinicalgenomics/balsamic:develop-somalier",
         DockerContainers.CNVPYTOR.value: "docker://clinicalgenomics/balsamic:develop-cnvpytor",
         DockerContainers.ALIGN_QC.value: "docker://clinicalgenomics/balsamic:develop-align_qc",