brocklab/pycashier issues and pull requests

#42 - Update pycashier to allow non-integer clustering ratios

Issue - State: closed - Opened by AndreaLGardner 4 months ago

#41 - add manuscript files to main

Pull Request - State: closed - Opened by daylinmorgan 5 months ago

#40 - fix(#37)

Pull Request - State: closed - Opened by daylinmorgan 5 months ago

#39 - improve startup/param output

Pull Request - State: closed - Opened by daylinmorgan 5 months ago

#38 - fix(#31): add support for overriding runtime dependencies

Pull Request - State: closed - Opened by daylinmorgan 5 months ago

#37 - "is complete" check should exit with code 0 if all samples are finished processing

Issue - State: closed - Opened by daylinmorgan 5 months ago

#36 - use pixi for docs generation and GHA

Pull Request - State: closed - Opened by daylinmorgan 5 months ago

#35 - docs(#29): add plaintext version of cli reference

Pull Request - State: closed - Opened by daylinmorgan 5 months ago

#34 - lift python version requirement to <= 3.12

Issue - State: closed - Opened by daylinmorgan 5 months ago

#33 - build: drop pdm for pixi only dev environment

Pull Request - State: closed - Opened by daylinmorgan 5 months ago

#32 - JOSS review tracking

Issue - State: open - Opened by daylinmorgan 5 months ago

#31 - allow overriding hardcoded executables

Issue - State: closed - Opened by daylinmorgan 5 months ago
Labels: enhancement

#30 - example usage of `pycashier`

Issue - State: open - Opened by daylinmorgan 5 months ago
Labels: documentation

#29 - the cli reference page should have plaintext versions

Issue - State: closed - Opened by daylinmorgan 5 months ago
Labels: documentation

#28 - erroneous debug print when saving config file

Issue - State: closed - Opened by daylinmorgan 6 months ago

#27 - Add more context to final filtering step

Issue - State: open - Opened by daylinmorgan 7 months ago

#26 - docs: expand README and add contributing guide

Pull Request - State: closed - Opened by daylinmorgan 10 months ago

#25 - pre-run-checks still too strict

Issue - State: closed - Opened by daylinmorgan 11 months ago

#24 - fix(#22): actually return candidate files

Pull Request - State: closed - Opened by daylinmorgan 11 months ago

#23 - build: switch to pixi for development

Pull Request - State: closed - Opened by daylinmorgan 11 months ago

#22 - --sample flag is broken

Issue - State: closed - Opened by daylinmorgan 11 months ago - 1 comment

#21 - pycashier fails to detect duplicate sample names in input dir

Issue - State: closed - Opened by daylinmorgan 12 months ago

#20 - major refactor and version bump

Pull Request - State: closed - Opened by daylinmorgan 12 months ago

#19 - add flag to assist users with storage limited systems

Issue - State: open - Opened by daylinmorgan over 1 year ago - 1 comment

#18 - slow to generate queue with many files

Issue - State: closed - Opened by daylinmorgan over 1 year ago

#17 - merge filename regex too stringent

Issue - State: closed - Opened by daylinmorgan over 1 year ago - 1 comment

#16 - pre-run check fail when they shouldn't

Issue - State: closed - Opened by daylinmorgan over 1 year ago

#15 - calls to `Path.mkdir` should include parents=True

Issue - State: closed - Opened by daylinmorgan about 2 years ago

#14 - pycashier isn't performing its `init check` to make sure `fastp`,`starcode` and `cutadapt` are in the path.

Issue - State: closed - Opened by daylinmorgan about 2 years ago

#13 - Python <3.10 is broken

Issue - State: closed - Opened by daylinmorgan about 2 years ago

#12 - pysam fails to read file when using `docker`

Issue - State: closed - Opened by daylinmorgan about 2 years ago

#11 - Add sample parameter

Issue - State: closed - Opened by daylinmorgan about 2 years ago - 1 comment
Labels: enhancement

#10 - pysam init check isn't needed if only using merge/extract/combine workflow

Issue - State: closed - Opened by daylinmorgan over 2 years ago

#9 - Ignoring hidden files

Issue - State: closed - Opened by daylinmorgan over 2 years ago

#8 - File detection before extraction

Issue - State: closed - Opened by daylinmorgan almost 3 years ago

#7 - Version 0.3.0 not on conda-forge yet because of dependency issues in recipe

Issue - State: closed - Opened by daylinmorgan almost 3 years ago

#6 - single cell update

Pull Request - State: closed - Opened by daylinmorgan over 4 years ago

#5 - change filter defaults and options

Pull Request - State: closed - Opened by daylinmorgan over 4 years ago

#4 - Pear merge

Pull Request - State: closed - Opened by daylinmorgan over 4 years ago

#3 - Update requirements.txt

Pull Request - State: closed - Opened by aedin over 4 years ago

#2 - non fastq file

Issue - State: closed - Opened by aedin over 4 years ago - 6 comments

#1 - Merge

Pull Request - State: closed - Opened by daylinmorgan over 4 years ago

GitHub / brocklab/pycashier issues and pull requests