https://github.com/clinical-genomics/crunchy

Compress fastq files with spring and check the integrity

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary

Keywords from Contributors

orchestrator

Last synced: 11 months ago · JSON representation

Repository

Compress fastq files with spring and check the integrity

Basic Info

Host: GitHub
Owner: Clinical-Genomics
License: mit
Language: Python
Default Branch: master
Size: 4.57 MB

Statistics

Stars: 2
Watchers: 7
Forks: 1
Open Issues: 3
Releases: 19

Created over 6 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License Codeowners

Crunchy

A python wrapper around spring and cram (samtools) to compress fastq to spring and bam to cram. When compressing fastqs to spring an integrity check can be performed by using flag: crunchy compress spring --spring-path <springfile> --first <read_1.fastq> --second <read_2.fastq> --check-integrity

Install

Pip

pip install crunchy

Docker

This will install crunchy as well as samtools and spring within the container. docker pull clinicalgenomics/crunchy:0.5 Run crunchy using: docker run clinicalgenomics/crunchy:0.5 crunchy

Developers

``` git clone https://github.com/Clinical-Genomics/crunchy pip install -e . crunchy --help Usage: crunchy [OPTIONS] COMMAND [ARGS]...

Base command for crunchy

            .---. .---.
           :     : o   :    me want cookie!
       _..-:   o :     :-.._    /
   .-''  '  `---' `---' "   ``-.
 .'   "   '  "  .    "  . '  "  `.
:   '.---.,,.,...,.,.,.,..---.  ' ;
`. " `.                     .' " .'
 `.  '`.                   .' ' .'
  `.    `-._           _.-' "  .'  .----.
    `. "    '"--...--"'  . ' .'  .'  o   `.
    .'`-._'    " .     " _.-'`. :       o  :
  .'      ```--.....--'''    ' `:_ o       :
.'    "     '         "     "   ; `.;";";";'

; ' " ' . ; .' ; ; ; ; ' ' ' " .' .-' ' " " ' " " _.-'

Options: --spring-binary TEXT Path to spring binary [default: spring] --samtools-binary TEXT Path to spring binary [default: samtools] -t, --threads INTEGER Number of threads to use for spring compression [default: 8] -r, --reference TEXT Path to reference genome --log-level [DEBUG|INFO|WARNING] Choose what log messages to show --tmp-dir TEXT If specific temp dir should be used --help Show this message and exit.

Commands: auto Run whole pipeline by compressing, comparing and deleting... compare Compare two files by generating checksums. compress Compress genomic files decompress Decompress genomic files ```

Workflow

Each command can be run separately. To compress all fastq pairs below a directory run crunchy auto spring <path_to_dir>.

Recursively find all fastq pairs
Compress all pairs with spring file_1.fastq + file_2.fastq (spring)-> file.spring
Decompress with spring file.spring (spring)-> file_1.spring.fastq + file_2.spring.fastq
Compare checksum with previous file_1.spring.fastq + file_1.fastq (hashlib)-> compare
Delete fastq (If the compression was lossless) file_1.fastq + file_2.fastq (rm)->

Owner

Name: Clinical Genomics
Login: Clinical-Genomics
Kind: organization
Location: Stockholm, Sweden

Website: https://clinical-genomics.github.io
Repositories: 67
Profile: https://github.com/Clinical-Genomics

GitHub Events

Total

Release event: 1
Watch event: 1
Issue comment event: 5
Push event: 2
Pull request event: 2
Create event: 3

Last Year

Release event: 1
Watch event: 1
Issue comment event: 5
Push event: 2
Pull request event: 2
Create event: 3

Committers

Last synced: over 3 years ago

All Time

Total Commits: 136
Total Committers: 3
Avg Commits per committer: 45.333
Development Distribution Score (DDS): 0.294

Top Committers

Name	Email	Commits
Måns Magnusson	m**n@s**e	96
henrikstranneheim	h**m@s**e	34
Clinical Genomics Bot	c**m@g**m	6

Committer Domains (Top 20 + Academic)

scilifelab.se: 2

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 6
Total pull requests: 32
Average time to close issues: 10 days
Average time to close pull requests: about 2 months
Total issue authors: 2
Total pull request authors: 4
Average comments per issue: 0.83
Average comments per pull request: 2.03
Merged pull requests: 27
Bot issues: 0
Bot pull requests: 3

Past Year

Issues: 0
Pull requests: 10
Average time to close issues: N/A
Average time to close pull requests: 4 days
Issue authors: 0
Pull request authors: 2
Average comments per issue: 0
Average comments per pull request: 3.4
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 1

View more stats

Top Authors

Issue Authors

moonso (5)
henrikstranneheim (1)

Pull Request Authors

henrikstranneheim (27)
moonso (11)
dependabot[bot] (4)
seallard (1)

Top Labels

Issue Labels

Pull Request Labels

dependencies (4) security (4)

Packages

Total packages: 1
Total downloads:
- pypi 92 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 13
Total maintainers: 3

pypi.org: crunchy

Compress fastq files with spring and check the integrity

Documentation: https://crunchy.readthedocs.io/
License: MIT
Latest release: 1.0.13
published over 1 year ago

Versions: 13
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 92 Last month

Rankings

Dependent packages count: 10.1%

Dependent repos count: 21.6%

Forks count: 22.6%

Average: 25.2%

Downloads: 32.7%

Stargazers count: 38.8%

Maintainers (3)

henriks karlnyr clingen

Last synced: 11 months ago

Dependencies

Pipfile pypi

black ==19.10b0 develop
crunchy * develop
flake8 * develop
pylint * develop
pytest * develop
pytest-cov * develop
pytest-mock * develop
click *
coloredlogs *

Pipfile.lock pypi

appdirs ==1.4.3 develop
astroid ==2.3.3 develop
attrs ==19.3.0 develop
black ==19.10b0 develop
click ==7.1.1 develop
coloredlogs ==14.0 develop
coverage ==5.1 develop
crunchy * develop
entrypoints ==0.3 develop
flake8 ==3.7.9 develop
humanfriendly ==8.1 develop
importlib-metadata ==1.6.0 develop
isort ==4.3.21 develop
lazy-object-proxy ==1.4.3 develop
mccabe ==0.6.1 develop
more-itertools ==8.2.0 develop
packaging ==20.3 develop
pathspec ==0.8.0 develop
pluggy ==0.13.1 develop
py ==1.8.1 develop
pycodestyle ==2.5.0 develop
pyflakes ==2.1.1 develop
pylint ==2.4.4 develop
pyparsing ==2.4.7 develop
pytest ==5.4.1 develop
pytest-cov ==2.8.1 develop
pytest-mock ==3.0.0 develop
regex ==2020.4.4 develop
six ==1.14.0 develop
toml ==0.10.0 develop
typed-ast ==1.4.1 develop
wcwidth ==0.1.9 develop
wrapt ==1.11.2 develop
zipp ==3.1.0 develop
click ==7.1.1
coloredlogs ==14.0
humanfriendly ==8.1

requirements.txt pypi

click *
coloredlogs *

.github/workflows/build_and_publish_pypi.yml actions

actions/checkout v2.5.0 composite
actions/setup-python v4.3.1 composite
pypa/gh-action-pypi-publish v1.5.1 composite

.github/workflows/bumpversion.yml actions

Clinical-Genomics/bump2version-ci v3 composite

.github/workflows/main.yml actions

actions/checkout v2.5.0 composite
conda-incubator/setup-miniconda v2.2.0 composite

.github/workflows/workflow-master.yaml actions

actions/checkout v2.5.0 composite
codecov/codecov-action v1 composite
conda-incubator/setup-miniconda v2.2.0 composite

container/Dockerfile docker

python 3.10-slim build

.github/workflows/black.yml actions

actions/checkout v4.1.1 composite
actions/setup-python v5 composite
psf/black stable composite

setup.py pypi

https://github.com/clinical-genomics/crunchy

Science Score: 26.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

Crunchy

Install

Pip

Docker

Developers

Workflow

Owner

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: crunchy

Rankings

Maintainers (3)

Dependencies