dgomezpere msm_tfm issues

dgomezpere / msm_tfm

Development of an application to visualize, annotate and prioritize somatic variants in cancer

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

#44 dgomezpere closed 2 years ago
0
[vcf_pipeline] Force VEP annotation in `--offline` mode

#43 dgomezpere closed 2 years ago
0
[app] Add a button to open panoptes in port `5000` when running an analysis

#42 dgomezpere closed 2 years ago
0
[app] New analysis view implementation

#41 dgomezpere opened 2 years ago
0
[app] Analysis list view implementation

#40 dgomezpere opened 2 years ago
2
[vcf_etl] Script to run mongo service in `/opt/scripts` and `/opt/bin` symlink

#39 dgomezpere opened 2 years ago
0
[vcf_etl] Property `length` from header.Coting object must be integer

#38 dgomezpere closed 2 years ago
0
[vcf_pipeline] Add the mongo_builder.py as a rule in the pipeline after VEP annotation

#37 dgomezpere closed 2 years ago
0
[vcf_etl] recordAnnotation should parse and convert to correct dtypes all the VEP fields

#36 dgomezpere opened 2 years ago
0
[vcf_pipeline%app] Implement `panoptes` for Snakemake pipeline monitoring

#35 dgomezpere opened 2 years ago
1
[docker%python] Add `dash`, `plotly`, `dash-bio` and `dash-bootstrap-components` in python requirements

#34 dgomezpere closed 2 years ago
0
[vcf_pipeline%scripts] Create a function in `vt_report_parser.py` to import as module in pipeline rules

#33 dgomezpere closed 2 years ago
0
[vcf_etl%vcf_record] Change `i` by `x` or `item`.

#32 segarmond closed 2 years ago
0
[vcf_pipeline] Document, design and implement `vcf_annotation.smk`

#31 dgomezpere closed 2 years ago
0
[vcf_pipeline%qc] Create VT report data parsers

#30 dgomezpere closed 2 years ago
1
[vcf_pipeline] Document, design and implement `vcf_qc_report.smk`

#29 dgomezpere closed 2 years ago
0
[docker%dockerfile] Install perl module DBD::mysql as a dependency of VEP

#28 dgomezpere closed 2 years ago
0
[vcf_etl%vcf_record] Set `value` variable as data type `list` for `VcfRecord.calls`

#27 segarmond closed 2 years ago
0
[vcf_etl%vcf_record] Set `value` variable as data type `RecordInfo`

#26 segarmond closed 2 years ago
0
[vcf_etl%vcf_record] Initialize `RecordInfo` with `vcfpy.record.INFO`

#25 segarmond closed 2 years ago
0
[vcf_etl%vcf_record] Rename variables `dictionary` and `vector` by `value`

#24 segarmond closed 2 years ago
0
[vcf_etl%vcf_record] Check if `call.data` returns an `OrderedDict`.

#23 segarmond closed 2 years ago
1
[vcf_etl%vcf_record] Remove comment "For each call"

#22 segarmond closed 2 years ago
0
[docker%dockerfile] Error while installing R

#21 segarmond opened 2 years ago
0
[vcf_pipeline] Document, design and implement `vcf_decomp_norm.smk`

#20 dgomezpere closed 2 years ago
0
[vcf_pipeline] Document, design and implement `vcf_validation.smk`

#19 dgomezpere closed 2 years ago
0
[vcf_pipeline] MVP for a VCF annotation pipeline

#18 dgomezpere closed 2 years ago
0
[vcf_etl%vcf_record] Document all docstrings (classes, methods and decorators)

#17 dgomezpere closed 2 years ago
0
[vcf_etl%vcf_record] Create a `RecordCall` class

#16 dgomezpere closed 2 years ago
2
[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 dgomezpere closed 2 years ago
3
[vcf_etl%vcf_record] Change names of private methods from `VcfRecord` class

#14 dgomezpere closed 2 years ago
1
[vcf_etl%vcf_record] Change `self._INFO` by `self._info`

#13 dgomezpere closed 2 years ago
1
[vcf_etl%vcf_record] Change decorator names to stick to our naming convention in the data models design

#12 dgomezpere closed 2 years ago
1
[vcf_etl%vcf_record] Remove `record` decorators from VcfRecord class

#11 dgomezpere closed 2 years ago
1
[vcf_etl%vcf_header] Document VcfHeader class, methods and decorators

#10 dgomezpere closed 2 years ago
0
[docker%dockerfile] Error while installing java

#9 segarmond opened 2 years ago
0
[docker] Restructure scripts and additional config files to allocate in separate dirs

#8 dgomezpere closed 2 years ago
0
[docker] Create a script to launch jupyter lab with one command

#7 dgomezpere closed 2 years ago
0
[docker%dockerfile] Error while installing R base

#6 segarmond closed 2 years ago
1
[docker] Add `/opt/bin` to `$PATH` in Dockerfile

#5 dgomezpere closed 2 years ago
1
[docker] Create users and groups in Dockerfile

#4 dgomezpere opened 2 years ago
0
[docker] Create VEP installer for docker

#3 dgomezpere closed 2 years ago
0
[docker] Create vcf_validator installer for docker

#2 dgomezpere closed 2 years ago
0
[docker] Create a docker for bioinfo development and production

#1 dgomezpere opened 2 years ago
0