refactor: Fix all dependencies to specific versions #1096
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Codecov ReportBase: 99.25% // Head: 99.31% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## develop #1096 +/- ##
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+ Coverage 99.25% 99.31% +0.05%
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Files 29 29
Lines 1755 1756 +1
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+ Hits 1742 1744 +2
+ Misses 13 12 -1
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This part was not flexible enough to allow the new dependency yaml structure: BALSAMIC/BALSAMIC/utils/cli.py Lines 453 to 457 in 36a66e8 |
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### Added: * PIP specific missing tools to config #1096 * Filtering script to remove normal variants from TIDDIT #1120 * Store TMB files in HK #1144 ### Changed: * Fixed all conda container dependencies #1096 * Changed --max_sv_size in VEP params to the size of chr1 for hg19 #1124 * Increased time-limit for sambamba_exon_depth and picard_markduplicates to 6 hours #1143 * Update cosmicdb to v97 #1147 * Updated read the docs with the changes relevant to mention #1153 ### Fixed: * Update cryptography version (39.0.1) due to security alert #1087 * Bump cryptography to v40.0.2 and gsutil to v5.23 #1154 * Pytest file saved in balsamic directory #1093 * Fix varcall_py3 container bcftools dependency error #1097 * AscatNgs container #1155
This PR:
Balsamic container not included as it depends on the release version.
Review and tests:
TN-WGS
TN-TGA
PIP specific dependencies (
cnvkit) are included now in theconfig.jsonfile