snakemake/snakemake issues and pull requests

#871 - Solver occasionally does not converge(?) so that the workflow does not start

Issue - State: closed - Opened by fischuu about 4 years ago - 8 comments
Labels: bug

#870 - MissingOutputException when using a remote directory as an output with S3

Issue - State: open - Opened by keller-mark about 4 years ago - 2 comments
Labels: bug

#823 - checkpoint: pipeline finishing early

Issue - State: open - Opened by nick-youngblut about 4 years ago - 25 comments
Labels: bug

#815 - directory flag not working with tibanna

Issue - State: open - Opened by gdeoli about 4 years ago - 12 comments
Labels: bug

#786 - snakemake>5.25: "Can't locate LWP/Simple.pm in @INC "

Issue - State: open - Opened by nick-youngblut about 4 years ago - 7 comments
Labels: bug

#778 - Using cluster profile leaves log files empty

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

#775 - Waiting for files with slurm, But file exists.

Issue - State: open - Opened by eHirchaud about 4 years ago - 6 comments
Labels: bug

#663 - Separate metadata and incomplete job tracking

Pull Request - State: closed - Opened by mhulsman over 4 years ago - 3 comments

#641 - Print shell cmds when using wrappers

Issue - State: open - Opened by fgvieira over 4 years ago - 11 comments
Labels: enhancement

#609 - checkpoint + temp

Issue - State: closed - Opened by nick-youngblut over 4 years ago - 6 comments
Labels: enhancement

#608 - ConnectionRefusedError: [Errno 111] Connection refused when snakemake `--report`

Issue - State: open - Opened by tiramisutes over 4 years ago - 1 comment

#592 - Preemption for tibanna and azure

Issue - State: open - Opened by johanneskoester over 4 years ago - 9 comments
Labels: enhancement

#576 - MissingOutputException with directory and GS remote provider

Issue - State: open - Opened by eric-czech over 4 years ago - 38 comments
Labels: bug

#574 - default remote prefix duplicated for checkpoint output on cloud

Issue - State: closed - Opened by aryarm over 4 years ago - 24 comments
Labels: bug

#533 - WIP: Azure Batch integration

Pull Request - State: closed - Opened by andreas-wilm over 4 years ago - 7 comments

#522 - using snakemake shadow rules to store temp files on local nodes

Issue - State: open - Opened by KamilSJaron over 4 years ago - 33 comments
Labels: bug

#517 - Report statistics/metadata runtimes are incorrect

Issue - State: open - Opened by mbhall88 over 4 years ago - 3 comments
Labels: bug

#502 - Benchmark to log real time of job

Issue - State: open - Opened by pbiology over 4 years ago - 1 comment
Labels: enhancement

#492 - Support alternate signal handling for killing shell processes

Pull Request - State: open - Opened by nh13 over 4 years ago - 2 comments

#482 - wildcard_constraints not honored by glob_wildcards

Issue - State: open - Opened by jmeppley over 4 years ago - 1 comment
Labels: bug

#466 - Snakemake max_version and version in addition to min_version

Issue - State: open - Opened by chrarnold over 4 years ago - 1 comment
Labels: enhancement

#466 - Snakemake max_version and version in addition to min_version

Issue - State: open - Opened by chrarnold over 4 years ago - 4 comments
Labels: enhancement

#452 - Not following links when looking at child outputs.

Pull Request - State: open - Opened by blaiseli over 4 years ago - 2 comments

#439 - Checkpoints that can be done in parallel are evaluated and executed sequentially

Issue - State: open - Opened by zuny26 over 4 years ago - 4 comments
Labels: bug

#425 - Add the rule name to finished logging statement

Pull Request - State: open - Opened by nh13 over 4 years ago - 5 comments

#392 - MissingRuleException on output from subworkflow

Issue - State: open - Opened by JackCaster almost 5 years ago - 4 comments
Labels: bug

#352 - Allow conda environment activation by name on a per-rule basis

Issue - State: open - Opened by sstadick almost 5 years ago - 20 comments
Labels: enhancement

#348 - Jupyter notebook integration leaves empty notebook files when notebook errors occur

Issue - State: open - Opened by dciarletta almost 5 years ago - 4 comments
Labels: bug

#345 - Conda activate not working on MacOS

Issue - State: open - Opened by jdossgollin almost 5 years ago - 20 comments
Labels: bug

#308 - Mandatory option `--cores` is breaking peoples workflows

Issue - State: open - Opened by HDembinski almost 5 years ago - 56 comments
Labels: bug

#304 - Combining --use-conda and --use-singularity fails in some cases

Issue - State: open - Opened by reslp almost 5 years ago - 12 comments
Labels: bug

#301 - Job groups and SLURM job arrays support

Issue - State: open - Opened by lpla almost 5 years ago - 30 comments
Labels: enhancement

#292 - Checkpoints slow in large workflows

Issue - State: open - Opened by jonaszierer almost 5 years ago - 10 comments
Labels: enhancement

#282 - offline snakemake --report

Issue - State: open - Opened by erblast almost 5 years ago - 14 comments
Labels: enhancement

#281 - Handle GPU ids

Issue - State: open - Opened by billbrod almost 5 years ago - 10 comments
Labels: enhancement

#262 - Add Singularity arguments for specific rules in Snakefile

Issue - State: open - Opened by mbhall88 almost 5 years ago - 22 comments
Labels: enhancement

#254 - Proposal: migrate vim-snakemake plugin to this Github org namespace

Issue - State: open - Opened by alerque almost 5 years ago - 1 comment

#230 - Make previous output files available as prevoutput

Pull Request - State: open - Opened by johanneskoester about 5 years ago - 3 comments

#187 - Add env vars

Pull Request - State: open - Opened by cmeesters about 5 years ago - 6 comments

#139 - Nix/Guix support

Issue - State: open - Opened by edmundmiller about 5 years ago - 5 comments
Labels: enhancement

#135 - dot -> Error: <stdin>: syntax error in line 1 near '

Issue - State: closed - Opened by nick-youngblut about 5 years ago - 9 comments
Labels: bug

#133 - onError/onSuccess for rules

Issue - State: open - Opened by dsnezhkov about 5 years ago - 6 comments
Labels: enhancement

#81 - Size log

Pull Request - State: open - Opened by troycomi over 5 years ago - 2 comments

#39 - Snakemake not able to see output files until I "ls" the output directory

Issue - State: open - Opened by danielseaton over 5 years ago - 11 comments

#1 - Research object support

Pull Request - State: open - Opened by johanneskoester over 5 years ago - 10 comments

GitHub / snakemake/snakemake issues and pull requests