snakemake/snakemake issues and pull requests

#3078 - chore(main): release 8.20.1

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 3 comments
Labels: autorelease: tagged

#3077 - fix: add testcase data to package files

Pull Request - State: closed - Opened by johanneskoester 6 months ago - 3 comments

#3076 - fix: skip asset download if files are already present

Pull Request - State: closed - Opened by johanneskoester 6 months ago - 2 comments

#3075 - snakemake: error: unrecognized arguments: --drmaa

Issue - State: closed - Opened by hsiehph 6 months ago - 1 comment
Labels: bug

#3074 - feat: allow skipping apptainer and conda tests if not available

Pull Request - State: closed - Opened by veprbl 6 months ago - 2 comments

#3073 - feat: MANIFEST.in: include tests/ in sdist

Pull Request - State: closed - Opened by veprbl 6 months ago - 2 comments

#3072 - fix: avoid downloading if assets are provided

Pull Request - State: closed - Opened by veprbl 6 months ago - 2 comments

#3071 - Local input/output files with storage-fs and slurm plugin

Issue - State: open - Opened by raphaelbetschart 6 months ago
Labels: bug

#3070 - chore(main): release 8.20.0

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 3 comments
Labels: autorelease: tagged

#3069 - chore(main): release 8.19.3

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 3 comments
Labels: autorelease: tagged

#3068 - chore(main): release 8.19.2

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 3 comments
Labels: autorelease: tagged

#3067 - fix: fix issues with misinterpretation of max-jobs-per-timespan and max-jobs-per-seconds

Pull Request - State: closed - Opened by johanneskoester 6 months ago - 2 comments

#3066 - chore: assert that jobcount is unrestricted if no max-jobs-per-timespan is set

Pull Request - State: closed - Opened by johanneskoester 6 months ago - 2 comments

#3065 - chore(main): release 8.19.1

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 3 comments
Labels: autorelease: tagged

#3064 - fix: Inconsistent Linting Output Formatting

Pull Request - State: closed - Opened by Kleinjohann 6 months ago - 2 comments

#3063 - Print a "stack trace" after a MissingInputException

Issue - State: open - Opened by thekswenson 6 months ago
Labels: enhancement

#3062 - fix: pip deployment path

Pull Request - State: closed - Opened by jakevc 6 months ago - 2 comments

#3061 - Consider supporting docker engine along with appraiser as --sdm option

Issue - State: open - Opened by jakevc 6 months ago - 1 comment
Labels: enhancement

#3060 - fix: return empty set if rate limiter at max

Pull Request - State: closed - Opened by fgvieira 6 months ago - 2 comments

#3059 - docs: Suppress autosectionlabel duplicate warnings and header level skipped warning

Pull Request - State: open - Opened by vandalt 6 months ago - 4 comments

#3058 - docs: update `doc-environment.yml` file and Documentation Setup documentation

Pull Request - State: closed - Opened by vandalt 6 months ago - 5 comments

#3057 - CLI args for `script`

Pull Request - State: closed - Opened by johanez 6 months ago - 3 comments

#3056 - fix: avoid error accessing superclass in ioutils

Pull Request - State: closed - Opened by johanneskoester 6 months ago - 3 comments

#3055 - Why can't it recognize file names containing just numbers?

Issue - State: open - Opened by xiasijian 6 months ago - 2 comments
Labels: bug

#3054 - `doc-environment.yml` file seems outdated

Issue - State: closed - Opened by vandalt 6 months ago - 1 comment
Labels: bug

#3053 - Verbose Warnings when building the docs

Issue - State: open - Opened by vandalt 6 months ago - 1 comment
Labels: bug

#3052 - docs: various documentation fixes

Pull Request - State: closed - Opened by vandalt 6 months ago - 3 comments

#3051 - chore(main): release 8.19.0

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 3 comments
Labels: autorelease: tagged

#3050 - feat: check consistency of output file mtimes (must be newer than input files)

Pull Request - State: closed - Opened by johanneskoester 6 months ago - 2 comments

#3049 - `$SLURM_JOB_ID` not set correctly in `remote-job-local-storage-prefix` when running snakemake in a SLURM job context (which many cluster environments require)

Issue - State: open - Opened by hermidalc 6 months ago - 6 comments
Labels: bug

#3031 - fix: use query from storage object in order to be able to reflect possible modifications (via StorageProvider.postprocess_query())

Pull Request - State: closed - Opened by johanneskoester 6 months ago - 2 comments

#3023 - When using snakemake >=8 with Python 3.11 (but not Python 3.12) certain rules erroneously don't run in hard to reproduce circumstances

Issue - State: open - Opened by corneliusroemer 6 months ago - 1 comment
Labels: bug

#3022 - docs: recommending raw strings to get rid of syntax warnings

Pull Request - State: closed - Opened by cmeesters 6 months ago - 2 comments

#3019 - Snakemake only submits one job at a time to SLURM and waits for job to complete before submitting another one when `jobs: unlimited`, `cores: all`, `max-jobs-per-second: 1`

Issue - State: open - Opened by hermidalc 6 months ago - 13 comments
Labels: bug

#3008 - Cannot test tests/test_script_py/scripts/test_explicit_import.py or tests/test_conda_python_3_7_script/test_script.py

Issue - State: open - Opened by peterjc 6 months ago
Labels: bug

#3003 - Common use case where each input file runs a checkpoint producing a batch unknown number of output files results causing increasing and huge snakemake memory usage (DAG memory leak or inefficient memory management?)

Issue - State: open - Opened by hermidalc 7 months ago
Labels: bug

#2997 - New default behavior of cores command line parameter uses host thread count to limit thread count for submitted jobs

Issue - State: open - Opened by simonwm 7 months ago - 8 comments
Labels: bug

#2996 - params dependent on dynamic resources raise InputFunctionException

Issue - State: open - Opened by simonwm 7 months ago
Labels: bug

#2995 - Lines without curly brackets in triple-quoted f-strings vanish

Issue - State: open - Opened by simonwm 7 months ago
Labels: bug

#2994 - The priority directive should support lambdas

Issue - State: open - Opened by nh13 7 months ago - 4 comments
Labels: enhancement

#2993 - fix: parse_config yaml using safe loader with datetime handler

Pull Request - State: open - Opened by ollie-bell 7 months ago - 7 comments

#2992 - snakemake exit with MissingOutputException when using `--immediate-submit`

Issue - State: closed - Opened by sirintra 7 months ago - 1 comment
Labels: bug

#2991 - feat: cached bulk DAG update for multiple cluster jobs at once (series-7)

Pull Request - State: open - Opened by epruesse 7 months ago - 4 comments

#2990 - continuous command execution with files marked as "update" recreates file every time.

Issue - State: open - Opened by brgstfzj 7 months ago
Labels: bug

#2989 - `*_NUM_THREADS` env vars not being passed to `shell()` function call in wrapper

Issue - State: open - Opened by hermidalc 7 months ago
Labels: bug

#2988 - tests: fix broken tests due to breaking changes in dependencies

Pull Request - State: closed - Opened by Hugovdberg 7 months ago - 4 comments

#2987 - docs: Change sha256 checksum in docs to more realistic example

Pull Request - State: closed - Opened by wimglenn 7 months ago - 6 comments

#2986 - Accept hyphens in config key given to CLI

Issue - State: open - Opened by cmkobel 7 months ago - 2 comments
Labels: enhancement

#2985 - fix: Wrong linenumbers reported when linting

Pull Request - State: closed - Opened by Kleinjohann 7 months ago - 2 comments

#2984 - Remote report generation

Issue - State: open - Opened by jakevc 7 months ago - 2 comments
Labels: enhancement

#2983 - Question of usage of explicit import of snakemake object from snakemake.scripts

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

#2982 - Temp files are not deleted for rule before checkpoint that is rerun after checkpoint with new data.

Issue - State: open - Opened by LeeBergstrand 7 months ago - 6 comments
Labels: bug

#2981 - Python rules do not support single quotes or spaces in path

Issue - State: open - Opened by Warggr 7 months ago - 8 comments
Labels: bug

#2980 - Regression of KeyError: <rule name>

Issue - State: open - Opened by lczech 7 months ago - 1 comment
Labels: bug, stale

#2979 - --shared-fs-usage parameter sets input or output separately

Issue - State: open - Opened by yeyun1999 7 months ago - 1 comment
Labels: enhancement, stale

#2978 - rsync sync the same file twice in same node

Issue - State: open - Opened by yeyun1999 7 months ago - 1 comment
Labels: bug

#2977 - git integration

Issue - State: open - Opened by zmbc 7 months ago
Labels: enhancement

#2976 - docs: Make it more clear that the cluster commands now require a plugin

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

#2975 - docs: Update installation.rst to recommend Miniforge instead of Mambaforge

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

#2974 - Custom logging messages no longer appear in log file

Issue - State: open - Opened by lczech 7 months ago - 4 comments
Labels: bug

#2973 - --quiet no longer prints summary

Issue - State: open - Opened by goi42 7 months ago - 1 comment
Labels: bug, stale

#2972 - fix: unawaited coroutine sanitize_local_storage_copies

Pull Request - State: closed - Opened by laf070810 7 months ago - 1 comment

#2971 - help for symlinks

Issue - State: open - Opened by AmelZulji 7 months ago - 3 comments
Labels: stale

GitHub / snakemake/snakemake issues and pull requests