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Development #162

Merged
merged 134 commits into from
Jul 16, 2024
Merged

Development #162

merged 134 commits into from
Jul 16, 2024

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epruesse
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@codecov
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codecov bot commented May 15, 2021 •
edited
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Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (e35de0f) 72.77% compared to head (ff24b02) 60.71%.

Additional details and impacted files 
@@             Coverage Diff             @@
##           master     #162       +/-   ##
===========================================
- Coverage   72.77%   60.71%   -12.07%     
===========================================
  Files          38       40        +2     
  Lines        4691     5221      +530     
===========================================
- Hits         3414     3170      -244     
- Misses       1277     2051      +774
Flag Coverage Δ
Core ?
Tools 60.71% <ø> (-1.94%) ⬇️

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

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@sonarqubecloud
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Kudos, SonarCloud Quality Gate passed!

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

No Coverage information No Coverage information
0.0% 0.0% Duplication

epruesse and others added 19 commits August 5, 2021 23:30
@epruesse
Add basic show stage params
f8fef72
@epruesse
Allow choice param with name
018432c
@epruesse
Allow references to be directories
117dd5d
@epruesse
Add count_subread, count_htseq and quant_salmon
4be7cac
@epruesse
Add {:all_prevs:}
52c50e0
@epruesse
Add file type tx.fasta
8dd271c
@epruesse
Fix TimeoutError != asyncio.TimeoutError (!!!)
f2d0d90
@epruesse
Add MultiQC stage
e20e7ad
@epruesse
Update STAR, Salmon and RSEM stages
0ed8752
@epruesse
Add FastP
0cbd498
@epruesse
RSEM: turn of credibility interval calculation - takes very long
d823280
@epruesse
Allow references to be leftmost item in stacks
06ab130
@epruesse
Fix part of exception written to stdout, not stderr
f96b3a7
@epruesse
Fix YmpConfigException not showing correct lines for sequences
fbed67a
@epruesse
Comment
cfdff90
@epruesse
Increase RSEM threads
2e79841
@epruesse
Increase download block size
b35f77c
@epruesse
Log cancelled or timeout during download
df750e6
@epruesse
Refactor reference stage system
b27478f
@sonarqubecloud
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sonarqubecloud bot commented Nov 8, 2022

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 76 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

epruesse added 17 commits October 18, 2023 11:00
@epruesse
fix: pandas deprecation warning
e9dceee
@epruesse
feat: enable slurm job cancelling
dd9a80b
@epruesse
fix(multiqc): python 3.12 not working yet
c8f63ca
@epruesse
fix(blast): avoid split blast results in subdir created by other rule
24c5b04
@epruesse
fix(snakemake): pass cores value again, snakemake change
e51f872
@epruesse
feat(yamlconfig): improve error message
0209e97
@epruesse
feat(snakemake): match version 7.32 (InOutput)
2709c95
@epruesse
Add missing file
f34090d
@epruesse
chore(conda): adjust environment.yaml pkg versions
3b6fbcb
@epruesse
fix(util/check_input): handle file error
bac43df
@epruesse
fix(blast): bug in new checkpoint usage
49f07d1
@epruesse
feat(cli/env-list): allow filtering installed/not-installed
2209bea
@epruesse
fix(cli/env-list): remove unimplemented options
c29ca13
@epruesse
feat(cli/env-list): allow showing more fields; black
db6d666
@epruesse
feat(cli/env-list): allow writing as CSV (machine readable)
ff24b02
@epruesse
Update environment.yaml
8c57c79
@epruesse
Pin Snakemake
05f05f6
@epruesse epruesse merged commit c61fcb3 into master Jul 16, 2024
1 of 5 checks passed
@sonarqubecloud SonarQubeCloud
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Quality Gate Failed Quality Gate failed

Failed conditions
1 Security Hotspot
19.3% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud

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@epruesse