roslin-variant
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mskcc
Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis
We found in [`roslin_resources.json`](https://github.com/mskcc/roslin-variant/blob/2.6.x/setup/bin/roslin_resources.json) that certain resources were identical between `AgilentExon_51MB_b37_v3` and `Agilent_v4_51MB_Human`. The baits files had the exact positional info and the targets files also had the exact same...
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.25.7 to 1.26.5. Release notes Sourced from urllib3's releases. 1.26.5 :warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap Fixed...
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot] avatar"){kind=avatar}
Bumps [pyyaml](https://github.com/yaml/pyyaml) from 5.2 to 5.4. Changelog Sourced from pyyaml's changelog. 5.4 (2021-01-19) yaml/pyyaml#407 -- Build modernization, remove distutils, fix metadata, build wheels, CI to GHA yaml/pyyaml#472 -- Fix for...
Bumps [jinja2](https://github.com/pallets/jinja) from 2.10.3 to 2.11.3. Release notes Sourced from jinja2's releases. 2.11.3 This contains a fix for a speed issue with the urlize filter. urlize is likely to be...
Add more columns to data_clinical.txt, using http://oncotree.mskcc.org/cdd/api/ to standardize column names if possible. - [ ] `MOUSE_CONTAMINATION` - For batches with at least 1 PDX sample, report fraction of sequenced...
parse_request_file will pick up any fields that have the keys in the string. PI will pick up sequencer: PITT
Do TMB calculation like DMP does (number of non-silent somatic events in analysis MAF ÷ number of bps in canonical exons covered by assay), and append to data_clinical using nomenclature...
- [x] Use http://oncotree.mskcc.org/cdd/api/ to update column header descriptions and metadata. - [x] Swap `SAMPLE_TYPE` and `SAMPLE_CLASS` if appropriate. Refer to https://github.com/mskcc/roslin-internal-services/issues/6 for description of the problem. - [ ]...
Run "msisensor msi" with 35M sites using both v0.2 and v0.6, and append results into data_clinical using nomenclature recommended in http://oncotree.mskcc.org/cdd/api/
Per author suggestions at - https://github.com/mozack/abra2/issues/21#issuecomment-409657543 - of relevance: We have not done thorough testing with anything beyond trios to date. Also, the local assembly graph is not allowed to...