snakemake/snakemake issues and pull requests

#3270 - feat: do not fail if --cache is active but no SNAKEMAKE_OUTPUT_CACHE env var is defined. Instead, print a warning that explains the options.

Pull Request - State: open - Opened by johanneskoester 23 days ago - 3 comments

#3269 - fix: print filenames with quotes around them in RuleException

Pull Request - State: open - Opened by royjacobson 24 days ago - 2 comments

#3268 - CLI documentation contains invalid dashes

Issue - State: open - Opened by lczech 24 days ago
Labels: bug

#3267 - perf: compare checksums of input files <= 1MB (before (10KB)

Pull Request - State: closed - Opened by johanneskoester 24 days ago - 2 comments

#3266 - perf: query updated input files in parallel

Pull Request - State: closed - Opened by johanneskoester 24 days ago - 2 comments

#3265 - fix: `--delete-all-output` ignores `--dry-run`

Pull Request - State: open - Opened by GaspardR 25 days ago - 2 comments

#3264 - `--delete-all-output` ignores `--dry-run`

Issue - State: open - Opened by GaspardR 25 days ago
Labels: bug

#3263 - fix: clone source git repos for source files that come from github or gitlab

Pull Request - State: open - Opened by johanneskoester 25 days ago - 2 comments

#3262 - feat: add support for validation of polars dataframe and lazyframe

Pull Request - State: open - Opened by fgvieira 25 days ago - 2 comments

#3261 - Workflow should not fail on clock skew

Issue - State: open - Opened by Redmar-van-den-Berg 25 days ago
Labels: bug

#3260 - fix: try to set mtime of http(s) source files if possible

Pull Request - State: open - Opened by johanneskoester 25 days ago - 2 comments

#3259 - fix: do not use outdated metadata for rerun triggers (only warn about it)

Pull Request - State: closed - Opened by johanneskoester 25 days ago - 2 comments

#3258 - fix: ensure that exceptions print storage queries instead of local copies of remote files

Pull Request - State: closed - Opened by johanneskoester 26 days ago - 2 comments

#3257 - Conda not found in containzerized container

Issue - State: open - Opened by pdimens 27 days ago - 1 comment
Labels: bug

#3256 - fix: Fix bug with checkpoint execution

Pull Request - State: closed - Opened by zmbc 30 days ago - 3 comments

#3255 - chore(main): release 8.27.2

Pull Request - State: open - Opened by github-actions[bot] about 1 month ago - 2 comments
Labels: autorelease: pending

#3254 - Input files from the future

Issue - State: open - Opened by lgrcia about 1 month ago - 1 comment
Labels: enhancement

#3254 - Input files from the future

Issue - State: open - Opened by lgrcia about 1 month ago - 1 comment
Labels: enhancement

#3253 - feat: lambda functions for priority in rules

Pull Request - State: open - Opened by TheSkyentist about 1 month ago - 1 comment

#3252 - global conda directive error: The package snakemake-storage-plugin-http is not installed

Issue - State: open - Opened by danpal96 about 1 month ago
Labels: bug

#3252 - global conda directive error: The package snakemake-storage-plugin-http is not installed

Issue - State: open - Opened by danpal96 about 1 month ago
Labels: bug

#3251 - Support for `uv` in the integrated package management?

Issue - State: open - Opened by adonath about 1 month ago - 1 comment
Labels: enhancement

#3250 - Catch error codes of commands executed under the shell directive

Issue - State: open - Opened by harrymatthews50 about 1 month ago - 1 comment
Labels: enhancement

#3250 - Catch error codes of commands executed under the shell directive

Issue - State: open - Opened by harrymatthews50 about 1 month ago - 1 comment
Labels: enhancement

#3249 - error libmamba Non-conda folder exists at prefix error while running snakemake

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

#3249 - error libmamba Non-conda folder exists at prefix error while running snakemake

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

#3248 - The issue with --apptainer-prefix and -d

Issue - State: open - Opened by jmzhang1911 about 1 month ago
Labels: bug

#3248 - The issue with --apptainer-prefix and -d

Issue - State: open - Opened by jmzhang1911 about 1 month ago
Labels: bug

#3247 - Error handling in snakemake scheduler

Issue - State: open - Opened by fujch7 about 1 month ago - 1 comment
Labels: enhancement

#3247 - Error handling in snakemake scheduler

Issue - State: open - Opened by fujch7 about 1 month ago - 1 comment
Labels: enhancement

#3246 - docs: Adds instructions for using syntax highlighting with lazy.nvim

Pull Request - State: closed - Opened by fonors about 1 month ago - 3 comments

#3246 - docs: Adds instructions for using syntax highlighting with lazy.nvim

Pull Request - State: closed - Opened by fonors about 1 month ago - 3 comments

#3245 - chore(main): release 8.27.1

Pull Request - State: closed - Opened by github-actions[bot] about 1 month ago - 3 comments
Labels: autorelease: tagged

#3244 - chore(main): release 8.27.0

Pull Request - State: closed - Opened by github-actions[bot] about 1 month ago - 3 comments
Labels: autorelease: tagged

#3244 - chore(main): release 8.27.0

Pull Request - State: closed - Opened by github-actions[bot] about 1 month ago - 3 comments
Labels: autorelease: tagged

#3243 - Using Multiple Rules from the Same Module Overwrites Aliases in Snakemake

Issue - State: open - Opened by JieWu-GitHub about 2 months ago
Labels: bug

#3243 - Using Multiple Rules from the Same Module Overwrites Aliases in Snakemake

Issue - State: open - Opened by JieWu-GitHub about 2 months ago
Labels: bug

#3242 - Add support for rule grouping to improve workflow organization

Issue - State: open - Opened by jiangyun-fun about 2 months ago
Labels: enhancement

#3242 - Add support for rule grouping to improve workflow organization

Issue - State: open - Opened by jiangyun-fun about 2 months ago
Labels: enhancement