snakemake snakemake issues

snakemake / snakemake

This is the development home of the workflow management system Snakemake. For general information, see

https://snakemake.github.io

MIT License

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issues

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Newest Most commented Recently updated Oldest Least commented Least recently updated

Separately specifying group job "width" and "depth"

#2931 kdm9 opened 7 hours ago
0
fix: parse f-string as-is from source

#2930 Hocnonsense opened 23 hours ago
0
docs: fix code block formatting

#2929 mbhall88 opened 1 day ago
1
fix: handling of missing attributes in input/output/params lists that have been guarded against misuse (sort, index)

#2928 johanneskoester closed 1 day ago
1
feat: add helpers for deferred input/output etc. item access

#2927 johanneskoester opened 2 days ago
2
fix: include more context to syntax errors when rule parsing fails (#2924)

#2926 NelisDrost opened 2 days ago
0
fix: add test to check it fails

#2925 fgvieira opened 2 days ago
0
Not enough context given in SyntaxError to debug problem

#2924 WeatherGod opened 5 days ago
0
onstart handler documentation

#2923 cefect closed 5 days ago
2
docs: fix bugs of params in rule bwa_map

#2922 manji2001 closed 1 day ago
0
feat: add `can_transfer_local_files` to executor plugin interface

#2921 jhiemstrawisc opened 1 week ago
0
Slow DAG postprocessing on high-latency filesystems

#2920 benjeffery opened 1 week ago
2
Issue with unlocking directory

#2919 n318162971 opened 1 week ago
0
feat: add helper functions to parse input files

#2918 fgvieira opened 1 week ago
1
feat: added snakemake.script.snakemake for type hinting

#2917 Hugovdberg opened 1 week ago
9
Snakemake check output before the end of jobs

#2916 Martoyl closed 1 week ago
3
chore(main): release 8.14.1

#2915 github-actions[bot] opened 1 week ago
1
Importing a Python module within a Snakemake module raises a `ModuleNotFoundError`

#2914 ezherman opened 2 weeks ago
2
docs: output files within output directories is an error (#2848)

#2913 NelisDrost opened 2 weeks ago
3
slurm job submission

#2912 xl5525 opened 2 weeks ago
15
slurm executor not printing logs on fail

#2911 pdimens opened 2 weeks ago
13
docs: update FAQ - recommend ensure function for failing on empty output

#2910 NelisDrost closed 2 weeks ago
2
chore(main): release 8.14.0

#2909 github-actions[bot] closed 2 weeks ago
2
Snakemake API

#2908 gilmorera opened 2 weeks ago
0
feat: support for default value specification when using lookup helper function

#2907 johanneskoester closed 3 weeks ago
1
chore(main): release 8.13.0

#2906 github-actions[bot] closed 3 weeks ago
2
Invalid choice: 'slurm-jobstep' (choose from 'local', 'd ryrun', 'touch')

#2905 radaniba closed 3 weeks ago
1
fix: add assets and use local file links to allow offline reports

#2904 fs82 opened 3 weeks ago
11
mem_mb parsing error in workflow profile

#2903 zhujack8 opened 3 weeks ago
2
docs: add badge for bioconda version

#2902 fgvieira closed 3 weeks ago
1
Error handling for pointing at non-existing script

#2901 KasperThystrup opened 4 weeks ago
0
file inclusion/exclusion control?

#2900 cefect opened 4 weeks ago
0
Runnning multiple instance of workflow on slurm causes Denial-of-Service

#2899 shashwatsahay closed 3 weeks ago
1
fix: fix quoting issues when passing complex apptainer args to spawned jobs

#2898 johanneskoester closed 1 month ago
1
fix: properly restrict scheduler if --jobs/-j is used (in contrast to --cores) in local execution

#2897 johanneskoester closed 1 month ago
1
--jobs does not consider --local-cores when executing localrules

#2896 ckrushton opened 1 month ago
1
fix: fix corner case bug in input function exception handling

#2895 johanneskoester closed 1 month ago
1
Module conflicts in workflows with a diamond-shape file structure

#2894 mramospe opened 1 month ago
0
More descriptive error message for AmbiguousRuleException and update Documentation: Ruleorder

#2893 KasperThystrup opened 1 month ago
0
Allow child rule to inherit localrule tag

#2892 twillis209 opened 1 month ago
0
Stop workflow (without error) if an output file is empty

#2891 davidecrs opened 1 month ago
1
chore(main): release 8.12.0

#2890 github-actions[bot] closed 1 month ago
2
snakemake --export-cwl doesn't actually export CWL

#2889 charmoniumQ opened 1 month ago
1
feat: add flag to mark files where path should not be modified

#2888 fgvieira closed 2 weeks ago
1
feat: Include parameters in extended benchmarks

#2887 fgvieira closed 1 month ago
1
Snakemake Pipeline Issue

#2886 AzlanNI closed 1 week ago
2
install snakemake using `pip install git+https://github.com/snakemake/snakemake`

#2885 liamxg opened 1 month ago
2
install error

#2884 liamxg closed 3 weeks ago
1
Progress report when downloading from storage provider

#2883 ntessore opened 1 month ago
3
--quiet settings not intuitive

#2882 pdimens opened 1 month ago
1