Snakemake-Profiles slurm issues

Snakemake-Profiles / slurm

Cookiecutter for snakemake slurm profile

MIT License

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issues

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Parse sinfo

#70 percyfal closed 3 years ago
0
Cookiecutter config

#69 percyfal closed 3 years ago
5
TypeError: '>' not supported between instances of 'NoneType' and 'NoneType' when claiming nodes=1 with walltime

#68 zihhuafang closed 2 years ago
2
Factor out cookiecutter_settings into module

#67 frankier closed 3 years ago
3
make slurm-status.py script stand-alone

#66 Hoeze closed 1 year ago
1
Move pandas import to _get_cluster_configuration, update snakemake

#65 percyfal closed 3 years ago
0
Remove dependency on pandas

#64 frankier closed 3 years ago
1
Reduce dependence upon cookiecutter

#63 frankier closed 3 years ago
1
Submission fails if memory UNIT is used (e.g. mem: 1000M)

#62 sschmeier closed 3 years ago
4
Behaviour with the `--cores` snakemake parameter

#61 tdido closed 3 years ago
4
why mixed python/python3

#60 kkmann closed 4 years ago
1
[pull] master from percyfal:master

#59 pull[bot] closed 4 years ago
0
Update tests

#58 percyfal closed 4 years ago
1
[pull] master from percyfal:master

#57 pull[bot] closed 4 years ago
0
Jobs failing to submit for longer than 3 hours

#56 moldach closed 4 years ago
2
Grouped jobs: KeyError: 'params'

#55 CharlesJB closed 4 years ago
8
Update slurm-submit.py

#54 Minhui-Chen closed 4 years ago
1
Move CI to github actions

#53 percyfal closed 4 years ago
0
Couple of questions

#52 chrarnold closed 3 years ago
4
multiple profiles for different projects?

#51 giovp closed 2 years ago
7
Check if job has params before formatting

#50 twrightsman closed 4 years ago
1
Slurm Profile fails to detect or remove incomplete output from cancelled jobs

#49 johnstonmj closed 3 years ago
2
Error submitting jobscript (exit code 1)

#48 lczech closed 3 years ago
4
[pull] master from percyfal:master

#47 pull[bot] closed 4 years ago
0
Not quite understanding how to use this

#46 proteins247 closed 4 years ago
5
localrules in profile?

#45 rneher closed 4 years ago
3
Revamptests

#44 percyfal closed 4 years ago
0
Add snakemake string pattern formatting

#43 racng closed 4 years ago
1
Priority / override order of parsing arguments to SLURM (sbatch)

#42 johnstonmj closed 4 years ago
2
Don't make directory if dirname is empty string

#41 percyfal closed 4 years ago
0
How to set output and error files?

#40 mufernando closed 4 years ago
9
Simplify and clean up test code

#39 percyfal closed 4 years ago
0
Threads to cpus per task

#38 percyfal closed 4 years ago
1
put cluster_config in config.yaml

#37 jos4uke closed 4 years ago
2
Change rulename -> rule

#36 maehler closed 4 years ago
0
Threads should map to "-c" instead of "-n"

#35 jdwheaton closed 4 years ago
6
Fix boolean conversion of advanced_argument_conversion option

#34 mwort closed 4 years ago
3
Refactor and merge slurm-submit.py and per-profile cluster-config file

#33 mwort closed 4 years ago
10
[pull] master from percyfal:master

#32 pull[bot] closed 4 years ago
0
slurm profile is dead

#31 cmeesters closed 2 years ago
9
mem-per-cpu

#30 dnlbauer closed 4 years ago
0
How to specify slurm error/output paths via profile

#29 johnstonmj closed 4 years ago
2
Create output/error folders after parsing cluster configuration

#28 twrightsman closed 4 years ago
0
Unit of time in cluster configs

#27 ManavalanG closed 4 years ago
4
[pull] master from percyfal:master

#26 pull[bot] closed 5 years ago
0
Can the profile correctly handle snakemake groups?

#25 SilasK closed 5 years ago
16
Is it possible to provide the --qos parameter via the slurm profile?

#24 didrikolofsson closed 4 years ago
4
How to use SLURM profile in combination with cluster.json

#23 claczny closed 4 years ago
2
correctly handle status responses of the form 'CANCELLED by <uid>'

#22 brendanf closed 5 years ago
0
Fixes to minor issues

#21 percyfal closed 5 years ago
0

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