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feat: concatenation #1069

Merged
merged 104 commits into from
Jun 1, 2023
Merged

feat: concatenation #1069

merged 104 commits into from
Jun 1, 2023

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ivadym
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@ivadym ivadym commented Jan 23, 2023 •
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This PR:

Added:

  • Concatenation of input fastqs

Review and tests:

  • Tests pass (available in Stage)

    • civilsole (TO, WGS) / Expected QC fail: PCT_60X = 0.004532
    • fleetjay (TN, WGS) / Expected QC fail: PCT_60X = 0.00836
    • setamoeba (TO, TGA)
    • unitedbeagle (TN, TGA)
    • uphippo (TO, UMI) (gi_cfdna_3.1) / Expected QC fail: GC dropout = 1.650392, PCT target bases 1000X = 0.861996
    • equalbug (TN, UMI) / Expected QC fail: GC dropout = 1.087173 vs 1.087309
    • acetuna (TO, TGA, QC workflow)
    • richpony (PON)

  • Code review

  • New code is executed and covered by tests, and test approve

Vadym Ivanchuk added 21 commits January 11, 2023 11:26
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codecov bot commented Jan 23, 2023 •
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Codecov Report

Patch coverage: 100.00% and project coverage change: -0.04 ⚠️

Comparison is base (4e6ac8c) 99.31% compared to head (f1ee6f2) 99.28%.

Additional details and impacted files 
@@             Coverage Diff             @@
##           develop    #1069      +/-   ##
===========================================
- Coverage    99.31%   99.28%   -0.04%     
===========================================
  Files           29       29              
  Lines         1757     1680      -77     
===========================================
- Hits          1745     1668      -77     
  Misses          12       12
Flag Coverage Δ
unittests 99.28% <100.00%> (-0.04%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
BALSAMIC/constants/workflow_rules.py 100.00% <ø> (ø)
BALSAMIC/commands/config/case.py 96.42% <100.00%> (-0.55%) ⬇️
BALSAMIC/commands/config/pon.py 94.73% <100.00%> (-0.51%) ⬇️
BALSAMIC/commands/run/analysis.py 99.04% <100.00%> (-0.01%) ⬇️
BALSAMIC/constants/common.py 100.00% <100.00%> (ø)
BALSAMIC/utils/cli.py 100.00% <100.00%> (ø)
BALSAMIC/utils/io.py 100.00% <100.00%> (ø)
BALSAMIC/utils/models.py 100.00% <100.00%> (ø)
BALSAMIC/utils/rule.py 94.89% <100.00%> (-0.08%) ⬇️

☔ View full report in Codecov by Sentry.
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@ivadym ivadym changed the base branch from develop to update-snakemake-version March 7, 2023 18:52
@ivadym ivadym changed the base branch from update-snakemake-version to develop March 8, 2023 17:02
@ivadym ivadym changed the base branch from develop to update-snakemake-version March 13, 2023 09:15
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sonarcloud bot commented Apr 11, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 2 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@ivadym ivadym changed the base branch from update-snakemake-version to develop April 13, 2023 14:57
@ivadym ivadym changed the base branch from develop to update-snakemake-version April 13, 2023 14:59
@mathiasbio mathiasbio self-requested a review June 1, 2023 11:58
mathiasbio
mathiasbio approved these changes Jun 1, 2023
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Great job! :) ✅

@ivadym ivadym mentioned this pull request Jun 1, 2023
Merged
3 tasks
Base automatically changed from update-snakemake-version to develop June 1, 2023 13:00
@ivadym ivadym linked an issue Jun 1, 2023 that may be closed by this pull request
Parallelise alignment per lane instead of on concatenated fastqs #1077
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@sonarcloud
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sonarcloud bot commented Jun 1, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 2 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@ivadym ivadym merged commit 9d2b30a into develop Jun 1, 2023
@ivadym ivadym deleted the feat/concatenation branch June 1, 2023 13:52
@ivadym ivadym linked an issue Jul 13, 2023 that may be closed by this pull request
Move concatenation from cg to BALSAMIC #993
Closed
4 tasks
@ivadym ivadym mentioned this pull request Jul 13, 2023
Closed
4 tasks
@ivadym ivadym mentioned this pull request Sep 29, 2023
Closed
@ivadym ivadym mentioned this pull request Nov 6, 2023
Merged
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@fevac fevac fevac left review comments

@mathiasbio mathiasbio mathiasbio approved these changes

@khurrammaqbool khurrammaqbool Awaiting requested review from khurrammaqbool

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Successfully merging this pull request may close these issues.

Parallelise alignment per lane instead of on concatenated fastqs Move concatenation from cg to BALSAMIC
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@ivadym @mathiasbio @fevac