Wytamma/snk issues and pull requests

#77 - If commit is not found workflow is still installed

Issue - State: open - Opened by Wytamma about 1 month ago
Labels: bug

#76 - Make the distinction of the snk and snk-cli more clear

Issue - State: closed - Opened by Wytamma 4 months ago
Labels: documentation

#75 - OSError: [Errno 39] Directory not empty: 'envs'

Issue - State: open - Opened by Wytamma 4 months ago

#74 - Gitpython - Snk-cli conflicts while writing pyproject

Issue - State: closed - Opened by Andyargueasae 4 months ago - 1 comment

#73 - Remove git from snk-cli

Issue - State: closed - Opened by Wytamma 5 months ago
Labels: publication

#72 - FileNotFoundError: Could not find SNK config file in workflow directory:

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

#71 - Print snake help fails on v8

Issue - State: closed - Opened by Wytamma 5 months ago
Labels: bug

#70 - Dependancies

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

#69 - Dependancy injection for isolated venvs

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

#68 - Support Snakemake v8

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

#67 - Snk cli refactor

Pull Request - State: closed - Opened by Wytamma 7 months ago

#66 - If `version` is in the snk file then commit hash should also be printed

Issue - State: closed - Opened by Wytamma 7 months ago - 1 comment

#65 - Cluster flag for snk

Issue - State: closed - Opened by Kobie-Kirven 7 months ago - 2 comments

#64 - None should be editable on editable install

Issue - State: closed - Opened by Wytamma 7 months ago

#63 - scripts folder in working dir is interpreted as scripts folder...

Issue - State: closed - Opened by Wytamma 7 months ago - 1 comment

#62 - Order of workflow options changes

Issue - State: closed - Opened by Wytamma 8 months ago
Labels: bug

#61 - :truck: rename pipeline to workflow

Pull Request - State: closed - Opened by Wytamma 8 months ago

#60 - update snk list

Issue - State: closed - Opened by Wytamma 8 months ago

#59 - Monkey patched parse_config is not used in submission to the HPC

Issue - State: closed - Opened by Wytamma 9 months ago - 1 comment

#58 - (singularity) conda info --json' returned non-zero exit status

Issue - State: closed - Opened by ktmeaton 9 months ago - 1 comment

#57 - Snakemake versioning leads to pulp dependency issue

Issue - State: closed - Opened by ConnorChato 9 months ago - 1 comment

#56 - 🐛 cli arg doesn't overwrite config if arg is default

Issue - State: closed - Opened by Wytamma 9 months ago - 2 comments
Labels: bug

#55 - snk-cli

Issue - State: closed - Opened by Wytamma 9 months ago - 1 comment
Labels: priority:high

#54 - snk.yaml CLI control

Issue - State: closed - Opened by Wytamma 9 months ago - 1 comment

#53 - Snakemake version 8

Issue - State: closed - Opened by Wytamma 9 months ago - 2 comments

#52 - Profile

Pull Request - State: closed - Opened by Wytamma 9 months ago

#51 - add eject command

Issue - State: closed - Opened by Wytamma 9 months ago - 2 comments
Labels: documentation

#50 - Install pipeline from commit SHA

Pull Request - State: closed - Opened by ktmeaton 9 months ago - 2 comments

#49 - Base envs

Issue - State: closed - Opened by Wytamma 10 months ago - 2 comments

#48 - rerun-triggers?

Issue - State: closed - Opened by Wytamma 10 months ago

#47 - lists are filtered out by script show

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

#46 - Script command

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

#45 - Make conda usage optional

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

#44 - ModuleNotFoundError: No module named 'rich'

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

#43 - filter output of --dag

Issue - State: closed - Opened by Wytamma about 1 year ago - 1 comment

#42 - Arbitrary snakemake parameters do not work

Issue - State: closed - Opened by mmcguffi about 1 year ago - 2 comments

#41 - Change working directory

Issue - State: closed - Opened by Wytamma about 1 year ago - 1 comment

#40 - Args should be passed to snakemake as yaml

Issue - State: closed - Opened by Wytamma about 1 year ago - 5 comments

#39 - add log flag

Issue - State: closed - Opened by Wytamma about 1 year ago - 1 comment

#38 - move .conda to $SNK_HOME

Issue - State: open - Opened by Wytamma about 1 year ago - 4 comments

#37 - --config is not overwriting the default values that are not null

Issue - State: closed - Opened by Wytamma about 1 year ago - 1 comment

#36 - include extra config in the config command

Issue - State: closed - Opened by Wytamma about 1 year ago

#35 - int not passed from cli as int

Issue - State: closed - Opened by Wytamma about 1 year ago - 1 comment

#34 - Env

Pull Request - State: closed - Opened by Wytamma over 1 year ago

#33 - replace .snk with snk.yaml

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

#32 - Extract envs from Snakefile

Issue - State: closed - Opened by Wytamma over 1 year ago - 1 comment
Labels: enhancement

#31 - CI failing due to missing tmp file...

Issue - State: closed - Opened by Wytamma over 1 year ago - 1 comment
Labels: bug

#30 - enum option type

Issue - State: closed - Opened by Wytamma over 1 year ago
Labels: enhancement, publication

#29 - ✨ Add --dag option to run

Pull Request - State: closed - Opened by Wytamma over 1 year ago - 1 comment

#28 - Can't force install pipeline when giving a custom --name

Issue - State: closed - Opened by Wytamma over 1 year ago
Labels: bug

#27 - if .snakemake exists don't delete

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

#26 - Install resource folder automatically if detected

Issue - State: closed - Opened by ammaraziz over 1 year ago - 6 comments
Labels: bug, enhancement

#25 - Dag

Issue - State: closed - Opened by Wytamma over 1 year ago
Labels: enhancement

#24 - rules

Issue - State: open - Opened by Wytamma over 1 year ago - 1 comment
Labels: enhancement

#23 - 🐛 pandas failed to active properly when install in pipenv env

Issue - State: closed - Opened by Wytamma over 1 year ago
Labels: bug

#22 - Be smarter about env and profile dirs

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

#21 - SNK_HOME and SNK_BIN don't work from cli

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

#20 - conda install

Issue - State: open - Opened by Wytamma over 1 year ago - 5 comments
Labels: help wanted, publication

#19 - Add containers

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

#18 - Handle non-standard files from .snk

Issue - State: closed - Opened by Wytamma over 1 year ago - 1 comment
Labels: publication

#17 - Add option to install local pipelines

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

#16 - Use the GitHub api to search for pipelines

Issue - State: open - Opened by Wytamma over 1 year ago

#15 - add a scaffold project option

Issue - State: open - Opened by Wytamma over 1 year ago - 2 comments

#14 - Non-standard Snakefile

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

#13 - isolated environments

Issue - State: closed - Opened by Wytamma over 1 year ago - 2 comments
Labels: documentation

#12 - add --lock/--no-lock

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

#11 - Config

Issue - State: closed - Opened by Wytamma over 1 year ago - 2 comments

#10 - Refactor pipeline_cli_factory into class

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

#9 - resources

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

#8 - Add profiles

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

#7 - add option it specify a non standard config location

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

#6 - check if bin in path

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

#5 - add web interface

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

#4 - Defaulting to user installation if not writeable

Issue - State: closed - Opened by Wytamma over 1 year ago - 1 comment
Labels: enhancement

#3 - None is passed to snakemake as 'None'

Issue - State: closed - Opened by Wytamma over 1 year ago - 1 comment
Labels: bug

#2 - add .snk config file for cli params/config

Issue - State: closed - Opened by Wytamma over 1 year ago - 1 comment
Labels: enhancement

#1 - install with user/repo

Issue - State: closed - Opened by Wytamma over 1 year ago
Labels: enhancement

GitHub / Wytamma/snk issues and pull requests