Skip to content

db_access: Added application QC collection and removed obsolete ppmSeq collection #236

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
kenissur wants to merge 3 commits into
base: master
Choose a base branch
from
Open

db_access: Added application QC collection and removed obsolete ppmSeq collection #236

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
3056368
db_access: Added application QC collection and removed obsolete ppmSe…
kenissur Jan 13, 2025
cf91c5a
Submodule update
ilyasoifer Jan 14, 2025
f0d8f9e
Update ugbio_utils
ilyasoifer Jan 14, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion ugbio_utils
Open in desktop
Submodule ugbio_utils updated 78 files
+7 −7 .devcontainer/build_docker/devcontainer.json
+1 −1 .devcontainer/cnv/devcontainer.json
+52 −0 .devcontainer/core/devcontainer.json
+1 −1 .devcontainer/featuremap/devcontainer.json
+1 −1 .devcontainer/methylation/devcontainer.json
+1 −1 .devcontainer/mrd/devcontainer.json
+3 −0 .devcontainer/post-create-commands.sh
+1 −1 .devcontainer/ppmseq/devcontainer.json
+1 −1 .devcontainer/single_cell/devcontainer.json
+1 −1 .devcontainer/srsnv/devcontainer.json
+3 −2 .pre-commit-config.yaml
+24 −6 README.md
+1 −1 pyproject.toml
+1 −1 src/cloud_utils/pyproject.toml
+1 −1 src/cnv/pyproject.toml
+8 −0 src/core/README.core.md
+3 −4 src/core/pyproject.toml
+12 −15 src/core/tests/unit/test_single_sample_qc_html_report.py
+5 −4 src/core/tests/unit/test_sorter_to_h5.py
+1 −1 src/core/tests/unit/vcfbed/test_vcftools.py
+1 −1 src/core/ugbio_core/flow_format/error_model.py
+2 −2 src/core/ugbio_core/flow_format/flow_based_read.py
+1 −1 src/core/ugbio_core/flow_format/simulator.py
+0 −52 src/core/ugbio_core/report_utils.py
+0 −0 src/core/ugbio_core/reports/__init__.py
+154 −0 src/core/ugbio_core/reports/report_utils.py
+15 −39 src/core/ugbio_core/reports/single_sample_qc_create_html_report.ipynb
+11 −19 src/core/ugbio_core/sorter_to_h5.py
+1 −1 src/featuremap/pyproject.toml
+1 −1 src/freec/pyproject.toml
+1 −1 src/hla_la/pyproject.toml
+11 −0 src/methylation/Dockerfile
+12 −13 src/methylation/pyproject.toml
+2 −2 src/methylation/tests/resources/input_for_html_report.h5
+12 −11 src/methylation/tests/system/test_methyldackel_qc_parsing.py
+36 −0 src/methylation/tests/unit/test_generate_methylation_report.py
+0 −29 src/methylation/tests/unit/test_methyldackel_create_qc_report.py
+36 −35 src/methylation/ugbio_methylation/concat_methyldackel_csvs.py
+44 −0 src/methylation/ugbio_methylation/generate_methylation_report.py
+32 −0 src/methylation/ugbio_methylation/globals.py
+976 −120 src/methylation/ugbio_methylation/reports/methyldackel_qc_report.ipynb
+8 −3 src/mrd/pyproject.toml
+3 −0 src/mrd/tests/resources/report/Pa_46.Pa_46_FreshFrozen.matched.intersection.parquet
+3 −0 src/mrd/tests/resources/report/Pa_46.Pa_67_FFPE.control.intersection.parquet
+3 −0 src/mrd/tests/resources/report/Pa_46_333_LuNgs_08.featuremap_df.parquet
+3 −0 src/mrd/tests/resources/report/Pa_46_FreshFrozen.ann.chr20.filtered.vcf
+3 −0 src/mrd/tests/resources/report/Pa_46_FreshFrozen.ann.chr20.filtered.vcf.tbi
+1,372 −0 src/mrd/tests/resources/report/Pa_46_matched_no_db.coverage.csv
+3 −0 src/mrd/tests/resources/report/Pa_67_FFPE.ann.chr20.filtered.vcf
+3 −0 src/mrd/tests/resources/report/Pa_67_FFPE.ann.chr20.filtered.vcf.tbi
+41 −0 src/mrd/tests/unit/test_generate_mrd_report.py
+264 −0 src/mrd/ugbio_mrd/generate_mrd_report.py
+0 −112 src/mrd/ugbio_mrd/mrd_utils.py
+0 −111 src/mrd/ugbio_mrd/prepare_data_from_mrd_pipeline.py
+6 −2 src/omics/README.omics.md
+2 −1 src/omics/pyproject.toml
+34,532 −0 src/omics/tests/resources/cromwell_pricelist.json
+16 −2 src/omics/tests/unit/test_compare_cromwell_omics.py
+93 −0 src/omics/tests/unit/test_omics_cache_path.py
+120 −0 src/omics/ugbio_omics/omics_cache_path.py
+1 −1 src/ppmseq/pyproject.toml
+16 −17 src/ppmseq/ugbio_ppmseq/ppmSeq_utils.py
+10 −9 src/ppmseq/ugbio_ppmseq/reports/ppmSeq_qc_report.ipynb
+2 −7 src/single_cell/pyproject.toml
+3 −0 src/single_cell/tests/resources/single_cell_qc_stats_with_sorter_json.scRNA.applicationQC.h5
+73 −0 src/single_cell/tests/resources/sorter_stats.json
+46 −1 src/single_cell/tests/unit/test_collect_statistics.py
+4 −4 src/single_cell/tests/unit/test_single_cell_qc_pipeline.py
+33 −2 src/single_cell/ugbio_single_cell/collect_statistics.py
+10 −9 src/single_cell/ugbio_single_cell/reports/single_cell_qc_report.ipynb
+2 −0 src/single_cell/ugbio_single_cell/sc_qc_dataclasses.py
+23 −41 src/single_cell/ugbio_single_cell/single_cell_qc_pipeline.py
+2 −2 src/srsnv/pyproject.toml
+12 −11 src/srsnv/ugbio_srsnv/reports/srsnv_report.ipynb
+40 −41 src/srsnv/ugbio_srsnv/srsnv_plotting_utils.py
+1 −1 src/srsnv/ugbio_srsnv/srsnv_training_utils.py
+1 −1 src/vcflite/Cargo.toml
+28 −136 uv.lock
4 changes: 2 additions & 2 deletions ugvc/utils/db_access.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ class Collections(Enum):
RUNS = "runs"
SAMPLES = "samples"
EXECUTIONS = "executions"
PPMSEQ = "ppmseq"
APPLICATION_QC = "application_qc"


def initialize_client() -> pymongo.MongoClient:
Expand Down Expand Up @@ -49,7 +49,7 @@ def initialize_client() -> pymongo.MongoClient:
collections[Collections.RUNS] = my_db["runs"]
collections[Collections.EXECUTIONS] = my_db["runs.executions"]
collections[Collections.SAMPLES] = my_db["runs.executions.samples"]
collections[Collections.PPMSEQ] = my_db["ppmseq_workflows_view"]
collections[Collections.APPLICATION_QC] = my_db["runs.executions.samples.applicationQc"]
else:
warnings.warn("Define PAPYRUS_ACCESS_STRING environmental variable to enable access to Papyrus")
warnings.warn(
Expand Down
Loading