snakemake/snakemake issues and pull requests

#2866 - remove --cluster from v8.x

Issue - State: open - Opened by conchoecia 10 months ago - 1 comment
Labels: enhancement, stale

#2865 - False detection of formatting issues.

Issue - State: open - Opened by agbioinformatics 10 months ago - 2 comments
Labels: bug, stale

#2864 - fix: parsing fstring with if else on params #2657

Pull Request - State: closed - Opened by sravel 10 months ago - 8 comments

#2863 - chore(main): release 8.11.3

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 2 comments
Labels: autorelease: tagged

#2862 - feat: support per rule shell exec setting via resources

Pull Request - State: open - Opened by johanneskoester 10 months ago - 2 comments

#2861 - wrong python path is used when running python script with named conda environment

Issue - State: open - Opened by Marcel-Mueck 10 months ago - 1 comment
Labels: bug, stale

#2860 - fix: show queries of remote storage files instead of local paths in summary

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2859 - fix: ignore errors when cleaning up runtime cache

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2858 - chore(main): release 8.11.2

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 2 comments
Labels: autorelease: tagged

#2857 - feat: Prefer papermill to nbconvert

Pull Request - State: open - Opened by zmbc 10 months ago - 18 comments

#2856 - feat: allow to set shell_exec (e.g. bash, sh, zsh) per rule

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 3 comments

#2855 - fix: bug when requesting extended benchmark with slurm

Pull Request - State: closed - Opened by fgvieira 10 months ago - 1 comment
Labels: bug

#2854 - fix: omit norun jobs when determining remote storage input file retrieval

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2853 - fix: small typo in error

Pull Request - State: closed - Opened by jjjermiah 10 months ago - 1 comment

#2852 - Feature/jjjermiah/doc update

Pull Request - State: closed - Opened by jjjermiah 10 months ago - 2 comments

#2851 - docs: fix typo and link for RO Crate

Pull Request - State: closed - Opened by sdruskat 10 months ago - 1 comment

#2850 - fix: check template rendering output for leaked input file paths

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2849 - chore(main): release 8.11.1

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 2 comments
Labels: autorelease: tagged

#2848 - document ChildIOException

Issue - State: open - Opened by rueberger 10 months ago
Labels: enhancement

#2847 - fix: use keyword arguments in `_IOFile.open`

Pull Request - State: closed - Opened by J-Wall 10 months ago - 1 comment

#2846 - `snakemake.io._IOFile.open` method doesn't use it's keyword arguments

Issue - State: closed - Opened by J-Wall 10 months ago
Labels: bug

#2845 - fix: remove non-empty local copies of remote storage dirs

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2844 - `keep_local` does not keep remote files locally

Issue - State: open - Opened by Hugovdberg 10 months ago
Labels: bug

#2843 - fix: checkpoints inside modules are overwritten

Pull Request - State: open - Opened by fgvieira 10 months ago - 6 comments
Labels: bug, help wanted

#2842 - fix: only download input for local jobs in the main process, not within remote groups

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2841 - ModuleNotFoundError: No module named 'asyncore'

Issue - State: open - Opened by PandengWang 10 months ago - 3 comments
Labels: bug, stale

#2840 - chore(main): release 8.11.0

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 2 comments
Labels: autorelease: tagged

#2839 - fix: retrieve files from storage if necessary when calling their open method (e.g. when accessing output files from a checkpoint)

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2838 - incompatibility with using `rules.rulename.output` and importing snakefile as a module, using `use rule a from somemodule as a with...`

Issue - State: open - Opened by LukaP-BB 10 months ago - 3 comments
Labels: bug

#2837 - Bind current working directory to container

Issue - State: open - Opened by fgvieira 10 months ago
Labels: enhancement

#2836 - Error when using wrappers and `use rule as`

Issue - State: open - Opened by fgvieira 10 months ago - 1 comment
Labels: bug

#2835 - question: SFTP options

Issue - State: open - Opened by SanVerb 10 months ago - 1 comment

#2834 - carbon footprint in report

Issue - State: open - Opened by daaaaande 10 months ago - 4 comments
Labels: enhancement, stale: contribution welcome

#2833 - chore: Update min version requirement for smart-open

Pull Request - State: closed - Opened by melund 10 months ago - 1 comment

#2832 - Incorrect shell command executed when defined within a loop.

Issue - State: open - Opened by ethan-shanahan 10 months ago - 9 comments
Labels: bug

#2831 - fix: replace pkg_resources for python 3.12

Pull Request - State: closed - Opened by branchvincent 10 months ago - 3 comments

#2830 - feat: add monitoring plugin interface

Pull Request - State: closed - Opened by cademirch 10 months ago - 15 comments

#2829 - fix: return set instead of list when just --quiet

Pull Request - State: closed - Opened by cademirch 10 months ago - 1 comment

#2828 - --cluster-config BsubInvocation Error

Issue - State: closed - Opened by suhridbuddha 10 months ago - 2 comments
Labels: bug, stale

#2827 - fix: Prevent binary log files to crash snakemake execution with `show-failed-logs`

Pull Request - State: closed - Opened by votti 10 months ago - 3 comments

#2826 - `--show-failed-logs` if binary file used as `log` file

Issue - State: open - Opened by votti 10 months ago
Labels: bug

#2825 - --dry-run --quiet fails on 8

Issue - State: closed - Opened by rueberger 10 months ago
Labels: bug

#2824 - --until not working with checkpoints

Issue - State: open - Opened by nkt97 10 months ago - 4 comments
Labels: bug

#2823 - fix: invalid extensions with multiext and cache (#1808)

Pull Request - State: closed - Opened by fgvieira 10 months ago - 1 comment

#2822 - Incomplete DAG with checkpoints

Issue - State: open - Opened by fgvieira 10 months ago - 4 comments
Labels: bug

#2821 - Make --cores a forbidden parameter if an executor is used.

Issue - State: open - Opened by sven0schuierer 10 months ago
Labels: enhancement

#2820 - Add possibility to provide empty default resources in a profile (as was possible with SnakeMake 7.x.x)

Issue - State: open - Opened by sven0schuierer 10 months ago
Labels: enhancement

#2819 - Using option --drmaa_logs crashes snakemake

Issue - State: open - Opened by sven0schuierer 10 months ago
Labels: bug

#2818 - Key Error: workflow/rules/common.smk, line 25: 'resource_config'

Issue - State: closed - Opened by Erythroxylum 10 months ago - 1 comment
Labels: bug

#2817 - docs: add snakemake and reportplugins to req.txt to show all cli options

Pull Request - State: closed - Opened by cademirch 10 months ago - 3 comments

#2816 - Services setup and teardown procedures with specific scripts and warmup time

Issue - State: open - Opened by raffienficiaud 10 months ago - 1 comment
Labels: enhancement

#2815 - chore(main): release 8.10.8

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 2 comments
Labels: autorelease: tagged

#2814 - fix: module prefix added twice on expand

Pull Request - State: closed - Opened by fgvieira 10 months ago - 1 comment
Labels: bug

#2813 - Missing All Flags section in Snakemake docs in at least several 8.x versions

Issue - State: closed - Opened by bskubi 10 months ago
Labels: bug

#2812 - CreateRuleException: The name xxxxx is already used by another rule

Issue - State: closed - Opened by pdimens 10 months ago
Labels: bug

#2811 - fix: retrieve inputs of local rules from storage even if they are intermediate results

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2810 - fix: extend workflow test suite by wildcards with slashes (in order to detect bugs that can occur in executors)

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2809 - fix: remove extra call to setup_logger()

Pull Request - State: open - Opened by cademirch 10 months ago - 4 comments

#2808 - Snakemake 8.9.0 on a singularity slurm cluster combination error

Issue - State: closed - Opened by tinu-t 10 months ago - 7 comments

#2807 - software deployment conda confusion

Issue - State: open - Opened by pdimens 10 months ago
Labels: bug

#2806 - fix: handle async method in cleanup_storage_objects

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2805 - fix: do not constrain group jobs by threads when submitting to remote

Pull Request - State: closed - Opened by johanneskoester 10 months ago - 1 comment

#2804 - Split a repository using Snakefile

Issue - State: open - Opened by lucaz88 10 months ago
Labels: enhancement

#2803 - fix: expand error on modules with prefix (#1614)

Pull Request - State: closed - Opened by fgvieira 10 months ago - 1 comment

#2802 - "module command not found" using Snakemake with Slurm

Issue - State: closed - Opened by kevinrue 10 months ago - 2 comments
Labels: bug

#2801 - SpawnedJobsArgFactory should allow executor more control over CLI options

Issue - State: closed - Opened by cademirch 11 months ago - 1 comment
Labels: enhancement

#2800 - fix: failure message in cleanup_metadata

Pull Request - State: closed - Opened by sjpfenninger 11 months ago - 2 comments

#2799 - chore(main): release 8.10.7

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 2 comments
Labels: autorelease: tagged

#2798 - Shell comand within if-else statement do not print when use "--print-compilation" arguemnt

Issue - State: open - Opened by y9c 11 months ago - 1 comment
Labels: bug, stale

#2797 - Duplicate Calls to log_handler in log-handler-script

Issue - State: open - Opened by Ash1One 11 months ago - 2 comments
Labels: bug

#2796 - chore(main): release 8.10.6

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 2 comments
Labels: autorelease: tagged

#2795 - fix: respect APPTAINER_CACHEDIR and allow env variables in --apptainer-prefix and --conda-prefix

Pull Request - State: closed - Opened by johanneskoester 11 months ago - 1 comment

#2794 - chore(main): release 8.10.5

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 2 comments
Labels: autorelease: tagged

#2793 - fix: properly delete local copies of storage files after remote jobs

Pull Request - State: closed - Opened by johanneskoester 11 months ago - 1 comment

#2792 - Working example for new version 8 API

Issue - State: open - Opened by standage 11 months ago - 3 comments

#2791 - snakemake function import error

Issue - State: open - Opened by nicholasprice79 11 months ago - 2 comments

#2790 - fix: only constrain by --max-threads if threads of job are already known

Pull Request - State: closed - Opened by johanneskoester 11 months ago - 1 comment

#2789 - Alternative Solutions for Running Snakemake on Slurm without Configuring MySQL Database

Issue - State: open - Opened by yangxiao1220 11 months ago - 3 comments
Labels: bug

#2788 - CreateCondaEnvironmentException with Mamba when creating a Conda environment from a Snakemake workflow

Issue - State: open - Opened by Ran485 11 months ago - 1 comment
Labels: bug, stale

#2787 - Can only use unpack() on list and dict,

Issue - State: open - Opened by odetteg 11 months ago - 2 comments
Labels: stale

#2786 - The Workflow class cannot be imported due to a circular import

Issue - State: open - Opened by msto 11 months ago - 1 comment
Labels: bug

#2785 - chore(main): release 8.10.4

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 2 comments
Labels: autorelease: tagged

#2784 - chore(main): release 8.10.3

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 2 comments
Labels: autorelease: tagged

#2783 - Use profile to send jobs on different partition (slurm cluster)

Issue - State: closed - Opened by KevinMer 11 months ago - 2 comments
Labels: enhancement

#2782 - Top of report.html pages not viewable when page is longer than screen

Issue - State: open - Opened by dirkjanvw 11 months ago - 2 comments
Labels: bug

#2781 - chore(main): release 8.10.2

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 2 comments
Labels: autorelease: tagged

#2780 - fix: use base64 encoding for passing default resources args to jobs

Pull Request - State: closed - Opened by johanneskoester 11 months ago - 1 comment

#2779 - Improving modularisation by allowing inputs from the main workflow into subworkflows

Issue - State: closed - Opened by irm-codebase 11 months ago - 4 comments
Labels: enhancement

#2778 - fix: use base64 encoding when passing resources and threads to remote jobs (this solves issues with complex quoted resources)

Pull Request - State: closed - Opened by johanneskoester 11 months ago - 1 comment

GitHub / snakemake/snakemake issues and pull requests