Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / snakemake/snakemake issues and pull requests

#1847 - fix: fixed typos

Pull Request - State: closed - Opened by fgvieira over 2 years ago - 1 comment

#1833 - --configfile uses absolute path when executing on GSL which causes jobs to fail

Issue - State: open - Opened by cademirch over 2 years ago - 7 comments
Labels: bug

#1817 - fix: wrong rule names when nesting module imports

Pull Request - State: closed - Opened by kpj over 2 years ago - 2 comments

#1816 - Linting interprets command string starting with / wrongly as path

Issue - State: open - Opened by seb-mueller over 2 years ago - 2 comments
Labels: bug

#1811 - Prebuild conda env does not activate in "script:" rule

Issue - State: closed - Opened by Jahysama over 2 years ago - 3 comments
Labels: bug

#1808 - multiext and cache fail if suffixes to not start with dot

Issue - State: closed - Opened by fgvieira over 2 years ago - 2 comments
Labels: bug

#1805 - using `source_path` in params always triggers unneeded rerun

Issue - State: open - Opened by li-yq over 2 years ago - 8 comments
Labels: bug

#1801 - GurobiError caused by pulp checking for all available licenses when snakemake is initialised

Issue - State: open - Opened by Tomkourou over 2 years ago - 4 comments
Labels: bug

#1800 - fix: remote-azblob-sasToken-Authorization

Pull Request - State: closed - Opened by RezaMadi over 2 years ago - 6 comments

#1794 - Snakemake Uploading output to azure blob storage with sas token

Issue - State: closed - Opened by RezaMadi over 2 years ago
Labels: bug

#1769 - Snakemake throws a PeriodicWildcardError for some long filenames

Issue - State: open - Opened by cklarhorst over 2 years ago - 1 comment
Labels: bug

#1763 - Snakemake interprets "--singularity-args" input as image file?

Issue - State: open - Opened by ipcamit over 2 years ago - 4 comments
Labels: bug

#1760 - rule option to automatically shorten pathnames passed to commands

Issue - State: open - Opened by notestaff over 2 years ago - 8 comments
Labels: enhancement

#1758 - Rule dependencies not updated when importing module

Issue - State: open - Opened by Redmar-van-den-Berg over 2 years ago - 2 comments
Labels: bug

#1758 - Rule dependencies not updated when importing module

Issue - State: open - Opened by Redmar-van-den-Berg over 2 years ago - 2 comments
Labels: bug

#1757 - Rule inheritance in modules not support

Issue - State: open - Opened by Redmar-van-den-Berg over 2 years ago - 3 comments
Labels: bug

#1751 - channel_priority non-strict as warning

Issue - State: closed - Opened by mfansler over 2 years ago - 1 comment
Labels: enhancement

#1740 - chore(deps): bump GoogleCloudPlatform/github-actions from 0.2.1 to 0.6.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 3 comments
Labels: dependencies

#1726 - glob_wildcards does not obey wildcard_constraints directive

Issue - State: closed - Opened by ASLeonard over 2 years ago - 2 comments
Labels: bug

#1716 - Dependency hell on ppcle architecture

Issue - State: open - Opened by drjbarker over 2 years ago - 3 comments
Labels: bug

#1709 - Deterministic DOT output for --dag/--rulegraph

Issue - State: closed - Opened by standage over 2 years ago - 3 comments
Labels: enhancement

#1709 - Deterministic DOT output for --dag/--rulegraph

Issue - State: closed - Opened by standage over 2 years ago - 3 comments
Labels: enhancement

#1708 - fix: processing in conda yaml and url bug

Pull Request - State: closed - Opened by ShogoAkiyama over 2 years ago - 8 comments

#1700 - Multi-thread DAG Build for Very Large Workflows?

Issue - State: open - Opened by guarelin over 2 years ago - 4 comments

#1697 - Report generation fails when script path contains wildcard

Issue - State: closed - Opened by gibsramen over 2 years ago - 2 comments
Labels: bug

#1694 - Announcement: Change in rerun behavior in Snakemake 7.8

Issue - State: open - Opened by johanneskoester over 2 years ago - 33 comments

#1688 - Bug accessing config variable from within the shell directive in a module

Issue - State: open - Opened by ImNotaGit over 2 years ago - 6 comments
Labels: bug

#1677 - Change in rerun behavior in 7.8.0

Issue - State: closed - Opened by BCArg over 2 years ago - 21 comments
Labels: bug

#1676 - fix: added minimal tests for Paramspace

Pull Request - State: open - Opened by psteinb almost 3 years ago - 10 comments

#1674 - Snakemake conda bug- command: conda env export --name

Issue - State: open - Opened by eeko-kon almost 3 years ago - 6 comments
Labels: bug

#1668 - CWL export: 'Job' object has no attribute 'conda_env_file'

Issue - State: open - Opened by zyzzyxdonta almost 3 years ago - 6 comments
Labels: bug

#1654 - Directory for `--profile` not resolving relative paths correctly

Issue - State: open - Opened by lczech almost 3 years ago - 5 comments
Labels: bug

#1654 - Directory for `--profile` not resolving relative paths correctly

Issue - State: open - Opened by lczech almost 3 years ago - 5 comments
Labels: bug

#1639 - feat: Support activating amendments in PEP

Pull Request - State: open - Opened by SichongP almost 3 years ago - 4 comments

#1632 - Relative import in python script not working when using a module from Gitlab

Issue - State: open - Opened by RomainFeron almost 3 years ago - 3 comments
Labels: bug

#1625 - test: test to evaluate pipelines that using modules that them self use modules.

Pull Request - State: open - Opened by Smeds almost 3 years ago - 4 comments

#1620 - Customizable timeouts for the ILP scheduler

Issue - State: open - Opened by ning-y almost 3 years ago - 2 comments
Labels: enhancement

#1619 - Why can't we run conda and run together in a rule?

Issue - State: closed - Opened by animesh-workplace almost 3 years ago - 4 comments

#1614 - Workflow error in module when using a prefix and 'expand' in a rule input

Issue - State: closed - Opened by RomainFeron almost 3 years ago - 1 comment
Labels: bug

#1607 - Raise exceptions in the interpreter to have the debugger catch them

Issue - State: open - Opened by xapple almost 3 years ago - 1 comment
Labels: enhancement

#1607 - Raise exceptions in the interpreter to have the debugger catch them

Issue - State: open - Opened by xapple almost 3 years ago - 1 comment
Labels: enhancement

#1604 - Merging input over 1 or more wildcards

Issue - State: open - Opened by gilmorera almost 3 years ago - 7 comments
Labels: enhancement

#1593 - Python error when creating subdirectories

Issue - State: closed - Opened by dhoconno almost 3 years ago - 9 comments
Labels: bug

#1591 - Additional methods to declare local rules

Issue - State: closed - Opened by troycomi almost 3 years ago - 3 comments
Labels: enhancement

#1587 - feat: Issue a warning when unsupported chracters are used in wildcard names

Pull Request - State: open - Opened by SichongP almost 3 years ago - 4 comments

#1585 - osx-arm64 404 failed

Issue - State: closed - Opened by romeopenheiro almost 3 years ago - 4 comments
Labels: bug

#1583 - Snakemake + Domino Data Lab

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

#1551 - feat: add remote plugin system

Pull Request - State: open - Opened by hwalinga almost 3 years ago - 2 comments

#1531 - chore: add testcase for issue #1460

Pull Request - State: open - Opened by johanneskoester almost 3 years ago - 1 comment

#1529 - feat: allow to set shell per rule via the `shell_exec` directive (see docs)

Pull Request - State: open - Opened by johanneskoester almost 3 years ago - 1 comment

#1521 - Singularity execution of Docker image without bash does not work

Issue - State: open - Opened by dominikburri almost 3 years ago - 6 comments
Labels: bug

#1502 - Request: better/centralized documentation on syntax

Issue - State: open - Opened by jlumpe almost 3 years ago - 2 comments
Labels: enhancement

#1469 - Higher priority rule is executed when not needed in ambiguous cases

Issue - State: open - Opened by kpj almost 3 years ago - 2 comments
Labels: bug

#1425 - In cluster mode unserializable parameter leads to all parameters deleted

Issue - State: open - Opened by mxposed almost 3 years ago - 1 comment
Labels: bug

#1421 - Support for AWS Batch

Issue - State: open - Opened by nh13 almost 3 years ago - 9 comments
Labels: enhancement

#1399 - Make Jupyter notebooks portable

Issue - State: open - Opened by djross22 about 3 years ago - 4 comments
Labels: enhancement

#1378 - Timestamps of output are reset to the time when the rule completes

Issue - State: open - Opened by dariober about 3 years ago - 4 comments
Labels: bug

#1374 - Greedy solver not chosen despite ILP `cbc` taking >6min and thus >10s

Issue - State: closed - Opened by corneliusroemer about 3 years ago - 4 comments
Labels: bug

#1355 - feat: Introduction of remote_prefix remotes

Pull Request - State: open - Opened by bcouturi about 3 years ago - 3 comments

#1335 - multiext support for named output

Issue - State: open - Opened by fgvieira about 3 years ago - 1 comment
Labels: enhancement

#1296 - feat: enable the registration of new executors from external packages.

Pull Request - State: open - Opened by johanneskoester about 3 years ago - 1 comment
Labels: WIP

#1256 - Line number of error is incorrect

Issue - State: open - Opened by dariober over 3 years ago - 3 comments
Labels: bug

#1256 - Line number of error is incorrect

Issue - State: closed - Opened by dariober over 3 years ago - 3 comments
Labels: bug

#1248 - Snakemake regularly falls asleep when running on cluster with slurm within tmux

Issue - State: open - Opened by corneliusroemer over 3 years ago - 12 comments
Labels: bug

#1227 - Snakemake stops submitting jobs on SLURM cluster

Issue - State: open - Opened by LiterallyUniqueLogin over 3 years ago - 4 comments
Labels: bug

#1224 - input.size_mb is wrong for remote files on GCP

Issue - State: open - Opened by szsctt over 3 years ago - 4 comments
Labels: bug

#1209 - panoptes workflow naming

Issue - State: open - Opened by nick-youngblut over 3 years ago - 5 comments
Labels: enhancement

#1204 - snakemake does not find mamba or conda

Issue - State: open - Opened by slambrechts over 3 years ago - 8 comments
Labels: bug

#1171 - can't use function returning dict with `params:`

Issue - State: open - Opened by grahamgower over 3 years ago - 4 comments
Labels: bug

#1157 - Snakemake wrappers require cluster nodes to contact github

Issue - State: open - Opened by lparsons over 3 years ago - 4 comments
Labels: bug

#1122 - Make parameters visible to input and output

Issue - State: open - Opened by snajder-r over 3 years ago - 12 comments
Labels: enhancement

#1111 - feat: Load config files using anyconfig

Pull Request - State: open - Opened by kpj over 3 years ago - 4 comments

#1106 - AmbiguousRuleException when there is no ambiguity

Issue - State: closed - Opened by dkuzminov over 3 years ago - 2 comments
Labels: bug

#1106 - AmbiguousRuleException when there is no ambiguity

Issue - State: closed - Opened by dkuzminov over 3 years ago - 2 comments
Labels: bug

#1104 - edge cases fail with `--generate-unit-tests`

Issue - State: open - Opened by aryarm over 3 years ago - 3 comments
Labels: bug

#1023 - ruleorder is randomly ignored

Issue - State: closed - Opened by sebschmi over 3 years ago
Labels: bug

#1023 - ruleorder is randomly ignored

Issue - State: closed - Opened by sebschmi over 3 years ago
Labels: bug

#1014 - conda/snakemake not detecting networkx or pygraphiz for reports

Issue - State: closed - Opened by pdimens over 3 years ago - 4 comments
Labels: bug

#1005 - --forceall and --forcerun should be propagated for group jobs (cloud execution)

Issue - State: closed - Opened by nigiord almost 4 years ago - 1 comment
Labels: bug

#1003 - pulp filling up /tmp to 100% for many jobs - with workaround?

Issue - State: closed - Opened by philippbayer almost 4 years ago - 4 comments
Labels: bug

#992 - Allow to run Tibanna executor with "open_browser=False"

Issue - State: closed - Opened by nigiord almost 4 years ago
Labels: enhancement

#991 - Snakemake depends on functionality in smart_open 3

Issue - State: closed - Opened by Redmar-van-den-Berg almost 4 years ago
Labels: bug

#986 - module 'snakemake.checkpoints' has no attribute 'register'

Issue - State: closed - Opened by mazzalab almost 4 years ago - 2 comments

#964 - Updated the rule for variant calling in the basic tutorial.

Pull Request - State: open - Opened by daagv almost 4 years ago - 1 comment

#962 - Integrate Snakemake rules with the Python module system

Issue - State: open - Opened by Hoeze almost 4 years ago - 1 comment
Labels: enhancement

#962 - Integrate Snakemake rules with the Python module system

Issue - State: open - Opened by Hoeze almost 4 years ago - 1 comment
Labels: enhancement

#956 - Import local module in script

Issue - State: open - Opened by Hugovdberg almost 4 years ago - 6 comments
Labels: enhancement

#944 - Suggestion to allow for extra commands on jobscript

Issue - State: closed - Opened by fgvieira almost 4 years ago - 1 comment

#944 - Suggestion to allow for extra commands on jobscript

Issue - State: closed - Opened by fgvieira almost 4 years ago - 1 comment

#914 - --configfile flag is broken in combination with Kubernetes and GS buckets

Issue - State: open - Opened by TheBready almost 4 years ago - 4 comments
Labels: bug

#912 - Missing job IDs when updating checkpoints

Issue - State: closed - Opened by fgvieira almost 4 years ago
Labels: bug

#891 - Pass --cluster-status by environment

Issue - State: closed - Opened by Phhere almost 4 years ago - 2 comments
Labels: enhancement

#880 - Suggested solution to lints

Issue - State: closed - Opened by colinbrislawn about 4 years ago - 4 comments

#872 - Bundle many small jobs into one larger job submission

Issue - State: closed - Opened by fischuu about 4 years ago - 22 comments
Labels: enhancement