dgomezpere/msm_tfm

Issues

• [vcf_pipeline%config] Change VEP default organism from `hsapiens` to `homo_sapiens`

  #44 opened 3 years ago by dgomezpere
  0

• [vcf_pipeline] Force VEP annotation in `--offline` mode

  #43 opened 3 years ago by dgomezpere
  0

• [app] Analysis list view implementation

  #40 opened 3 years ago by dgomezpere
  2

• [app] Add a button to open panoptes in port `5000` when running an analysis

  #42 opened 3 years ago by dgomezpere
  0

• [vcf_pipeline%app] Implement `panoptes` for Snakemake pipeline monitoring

  #35 opened 3 years ago by dgomezpere
  1

• [vcf_pipeline] Add the mongo_builder.py as a rule in the pipeline after VEP annotation

  #37 opened 3 years ago by dgomezpere
  0

• [vcf_etl] Property `length` from header.Coting object must be integer

  #38 opened 3 years ago by dgomezpere
  0

• [vcf_etl%vcf_record] Create a `RecordInfo` class to store the key-value mapping of the INFO field of a vcfpy.record.Record object

  #15 opened 3 years ago by dgomezpere
  3

• [app] New analysis view implementation

  #41 opened 3 years ago by dgomezpere
  0

• [vcf_etl] Script to run mongo service in `/opt/scripts` and `/opt/bin` symlink

  #39 opened 3 years ago by dgomezpere
  0

• [docker%python] Add `dash`, `plotly`, `dash-bio` and `dash-bootstrap-components` in python requirements

  #34 opened 3 years ago by dgomezpere
  0

• [vcf_etl] recordAnnotation should parse and convert to correct dtypes all the VEP fields

  #36 opened 3 years ago by dgomezpere
  0

• [vcf_pipeline] MVP for a VCF annotation pipeline

  #18 opened 3 years ago by dgomezpere
  0

• [vcf_pipeline] Document, design and implement `vcf_qc_report.smk`

  #29 opened 3 years ago by dgomezpere
  0

• [vcf_pipeline%scripts] Create a function in `vt_report_parser.py` to import as module in pipeline rules

  #33 opened 3 years ago by dgomezpere
  0

• [vcf_pipeline%qc] Create VT report data parsers

  #30 opened 3 years ago by dgomezpere
  1

• [vcf_etl%vcf_record] Change `i` by `x` or `item`.

  #32 opened 3 years ago by segarmond
  0

• [vcf_pipeline] Document, design and implement `vcf_annotation.smk`

  #31 opened 3 years ago by dgomezpere
  0

• [vcf_etl%vcf_record] Document all docstrings (classes, methods and decorators)

  #17 opened 3 years ago by dgomezpere
  0

• [vcf_etl%vcf_record] Set `value` variable as data type `list` for `VcfRecord.calls`

  #27 opened 3 years ago by segarmond
  0

• [vcf_pipeline] Document, design and implement `vcf_decomp_norm.smk`

  #20 opened 3 years ago by dgomezpere
  0

• [vcf_pipeline] Document, design and implement `vcf_validation.smk`

  #19 opened 3 years ago by dgomezpere
  0

• [vcf_etl%vcf_record] Initialize `RecordInfo` with `vcfpy.record.INFO`

  #25 opened 3 years ago by segarmond
  0

• [vcf_etl%vcf_record] Check if `call.data` returns an `OrderedDict`.

  #23 opened 3 years ago by segarmond
  1

• [vcf_etl%vcf_header] Document VcfHeader class, methods and decorators

  #10 opened 3 years ago by dgomezpere
  0

• [vcf_etl%vcf_record] Create a `RecordCall` class

  #16 opened 3 years ago by dgomezpere
  2

• [docker%dockerfile] Install perl module DBD::mysql as a dependency of VEP

  #28 opened 3 years ago by dgomezpere
  0

• [vcf_etl%vcf_record] Set `value` variable as data type `RecordInfo`

  #26 opened 3 years ago by segarmond
  0

• [vcf_etl%vcf_record] Rename variables `dictionary` and `vector` by `value`

  #24 opened 3 years ago by segarmond
  0

• [vcf_etl%vcf_record] Remove comment "For each call"

  #22 opened 3 years ago by segarmond
  0

• [vcf_etl%vcf_record] Change names of private methods from `VcfRecord` class

  #14 opened 3 years ago by dgomezpere
  1

• [vcf_etl%vcf_record] Change decorator names to stick to our naming convention in the data models design

  #12 opened 3 years ago by dgomezpere
  1

• [vcf_etl%vcf_record] Remove `record` decorators from VcfRecord class

  #11 opened 3 years ago by dgomezpere
  1

• [vcf_etl%vcf_record] Change `self._INFO` by `self._info`

  #13 opened 3 years ago by dgomezpere
  1

• [docker%dockerfile] Error while installing R

  #21 opened 3 years ago by segarmond
  0

• [docker%dockerfile] Error while installing java

  #9 opened 3 years ago by segarmond
  0

• [docker] Create a script to launch jupyter lab with one command

  #7 opened 3 years ago by dgomezpere
  0

• [docker] Restructure scripts and additional config files to allocate in separate dirs

  #8 opened 3 years ago by dgomezpere
  0

• [docker] Create a docker for bioinfo development and production

  #1 opened 3 years ago by dgomezpere
  0

• [docker] Create VEP installer for docker

  #3 opened 3 years ago by dgomezpere
  0

• [docker] Add `/opt/bin` to `$PATH` in Dockerfile

  #5 opened 3 years ago by dgomezpere
  1

• [docker%dockerfile] Error while installing R base

  #6 opened 3 years ago by segarmond
  1

• [docker] Create vcf_validator installer for docker

  #2 opened 3 years ago by dgomezpere
  0

• [docker] Create users and groups in Dockerfile

  #4 opened 3 years ago by dgomezpere
  0