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refactor: Remove Balsamic container #1230

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Aug 16, 2023
Merged

refactor: Remove Balsamic container #1230

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2 changes: 0 additions & 2 deletions .bumpversion.cfg
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Expand Up @@ -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]
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2 changes: 1 addition & 1 deletion .github/workflows/docker_build_push.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .github/workflows/docker_build_push_release.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .github/workflows/docker_build_test_pull_request.yml
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Expand Up @@ -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
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1 change: 0 additions & 1 deletion BALSAMIC/constants/cache.py
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Expand Up @@ -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"
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34 changes: 0 additions & 34 deletions BALSAMIC/containers/balsamic/Dockerfile
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This file was deleted.

Empty file removed BALSAMIC/containers/balsamic/__init__.py
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1 change: 0 additions & 1 deletion BALSAMIC/containers/balsamic/balsamic.sh
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9 changes: 0 additions & 9 deletions BALSAMIC/containers/balsamic/balsamic.yaml
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2 changes: 0 additions & 2 deletions BALSAMIC/snakemake_rules/concatenation/concatenation.rule
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Expand Up @@ -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,
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2 changes: 0 additions & 2 deletions BALSAMIC/snakemake_rules/quality_control/qc_metrics.rule
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Expand Up @@ -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:
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2 changes: 0 additions & 2 deletions BALSAMIC/snakemake_rules/quality_control/report.rule
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Expand Up @@ -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:
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2 changes: 2 additions & 0 deletions CHANGELOG.rst
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@@ -1,5 +1,6 @@
[X.X.X]
-------

Added:
^^^^^^
* Fastq concatenation https://github.com/Clinical-Genomics/BALSAMIC/pull/1069
Expand Down Expand Up @@ -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/1230

[12.0.2]
--------
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1 change: 0 additions & 1 deletion tests/conftest.py
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Expand Up @@ -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",
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