Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Development #162

Open
wants to merge 132 commits into
base: master
Choose a base branch
from
Open

Development #162

wants to merge 132 commits into from

Conversation

epruesse
Copy link
Owner

No description provided.

@codecov
Copy link

codecov bot commented May 15, 2021 •
edited

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.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@sonarcloud
Copy link

sonarcloud bot commented May 18, 2021

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
@sonarcloud
Copy link

sonarcloud 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
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
@sonarcloud SonarCloud
Copy link

sonarcloud bot commented Dec 12, 2023

Quality Gate Failed Quality Gate failed

Failed conditions

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

See analysis details on SonarCloud

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
1 participant
@epruesse