StackOverflow Questions for Tag: snakemake

tgbrooks

Reputation: 311

Snakemake: using workflow.source_path with apptainer containers

snakemakesingularity-containerapptainer

Score: 0

Answers: 0

user24790338

Reputation: 3

Snakemake rules that are dependent on checkpoint outputs skipped

snakemakecheckpoint

Score: 0

Answers: 0

Devin Burke

Reputation: 538

How to allocate a GPU for snakemake 8 execution on GKE

kubernetesgoogle-kubernetes-enginesnakemake

Score: 0

Answers: 0

Sergio

Reputation: 107

How to run Snakemake >= 8 on a Slurm cluster?

cluster-computingslurmsnakemake

Score: 8

Answers: 1

Pida

Reputation: 15

different paths in Snakemake output

snakemake

Score: 0

Answers: 1

LittleByBlue

Reputation: 454

Snakemake fails to execute the preample when executing --edit-notebook inside a virtualenv

pythonjupyter-notebookvirtualenvsnakemake

Score: 0

Answers: 1

Wei-Chen Pan

Reputation: 3

User Error after running GATK BaseRecalibrator for WGS BAM file

snakemakegatk

Score: 0

Answers: 0

el-xefe

Reputation: 11

Run many wildcard rules one-after-the-other sequentially rather than in parallel?

parallel-processingsnakemakesnakemake-slurm

Score: 1

Answers: 1

RipollJ

Reputation: 13

Conda 4.10.3 and Snakemake >5 "__conda_exe" problem

condasnakemake

Score: 1

Answers: 2

ManJi

Reputation: 107

Why will the rule with `ln` in script be triggered even if I didn't change any of the code in Snakemake?

pythonsnakemake

Score: 0

Answers: 0

Yotam Feldman

Reputation: 43

Snakemake remote rule stalling before executing script in PBS cluster

cluster-computingsnakemakehpcpbs

Score: 1

Answers: 1

ManJi

Reputation: 107

How to prevent rule execution due to missing benchmark file in Snakemake?

pythonsnakemake

Score: 0

Answers: 1

Rboreal_Frippery

Reputation: 2318

Zip input and output without wildcards, using absolute paths

pythonsnakemake

Score: 0

Answers: 1

ninthpower

Reputation: 1765

Coupling inputs and outputs without shared wildcards

pythonsnakemake

Score: 1

Answers: 1

xie186

Reputation: 509

In .snakemake/singularity/, how to know which simg file corresponding to which docker image?

snakemakesingularity-container

Score: 0

Answers: 0

ManJi

Reputation: 107

When using the `name` directive, is there a way to get the rule name in `rules` in Snakemake?

pythonsnakemake

Score: 2

Answers: 0

Amel

Reputation: 1

Best practice for expanding parameters with multiple values

snakemake

Score: 0

Answers: 2

ManJi

Reputation: 107

Is it possible to conveniently get the command content generated by `shell()` in Snakemake?

pythonsnakemake

Score: 1

Answers: 0

Whitehot

Reputation: 497

Awk return success code on exit to snakemake

awksnakemake

Score: 0

Answers: 1

Harry Matthews

Reputation: 153

How to make a snakemake workflow in pure python?

pythonsnakemake

Score: 1

Answers: 0

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StackOverflow Questions for Tag: snakemake

Snakemake: using workflow.source_path with apptainer containers

Snakemake rules that are dependent on checkpoint outputs skipped

How to allocate a GPU for snakemake 8 execution on GKE

How to run Snakemake &gt;= 8 on a Slurm cluster?

different paths in Snakemake output

Snakemake fails to execute the preample when executing --edit-notebook inside a virtualenv

User Error after running GATK BaseRecalibrator for WGS BAM file

Run many wildcard rules one-after-the-other sequentially rather than in parallel?

Conda 4.10.3 and Snakemake &gt;5 &quot;__conda_exe&quot; problem

Why will the rule with `ln` in script be triggered even if I didn&#39;t change any of the code in Snakemake?

Snakemake remote rule stalling before executing script in PBS cluster

How to prevent rule execution due to missing benchmark file in Snakemake?

Zip input and output without wildcards, using absolute paths

Coupling inputs and outputs without shared wildcards

In .snakemake/singularity/, how to know which simg file corresponding to which docker image?

When using the `name` directive, is there a way to get the rule name in `rules` in Snakemake?

Best practice for expanding parameters with multiple values

Is it possible to conveniently get the command content generated by `shell()` in Snakemake?

Awk return success code on exit to snakemake

How to make a snakemake workflow in pure python?

How to run Snakemake >= 8 on a Slurm cluster?

Conda 4.10.3 and Snakemake >5 "__conda_exe" problem

Why will the rule with `ln` in script be triggered even if I didn't change any of the code in Snakemake?