Usage

Basic Usage

Navigate to your Snakemake pipeline directory and run:

cd /path/to/my/pipeline
charmer

The TUI will display jobs from .snakemake/metadata/ and scheduler queries.

Running Alongside Snakemake

Start your pipeline in one terminal:

snakemake --profile slurm -j 100

In another terminal, start charmer:

charmer

Charmer automatically detects new jobs as Snakemake submits them.

Interface

┌─────────────────────────────────────────────────────────────────────────────┐
│ charmer                              Running  01:23:45                      │
├─────────────────────────────────────────────────────────────────────────────┤
│ ██████████████████████░░░░░░░░░░░░░░  42/100 jobs  42%                     │
├─────────────────────────────────────────────────────────────────────────────┤
│ 12 Pending │ 8 Running │ 38 Done │ 1 Failed │ Filter: All │ Sort: Status  │
├───────────────────────────────────┬─────────────────────────────────────────┤
│ Jobs (3/54)                       │ Job Details                             │
│ ──────────────────────────────────│─────────────────────────────────────────│
│   ● align_reads[sample=S1]        │ Rule: align_reads                       │
│   ● align_reads[sample=S2]        │ SLURM Job: 12345678                     │
│ > ✗ call_variants[chr=chr1]       │ Node: node01                            │
│   ◐ merge_vcfs                    │ Status: Failed (exit 1)                 │
│   ○ annotate_variants             │ Runtime: 05:23                          │
│                                   │ CPUs: 4 | Memory: 32GB                  │
├───────────────────────────────────┴─────────────────────────────────────────┤
│ j/k:navigate  f:filter  s:sort  ?:help  q:quit                              │
└─────────────────────────────────────────────────────────────────────────────┘

Status Symbols

Symbol	Status
○	Pending
◐	Queued
●	Running
✓	Completed
✗	Failed
⊘	Cancelled

Keyboard Shortcuts

Navigation

Key	Action
j / ↓	Move down
k / ↑	Move up
g / Home	Go to first job
G / End	Go to last job

Filtering & Sorting

Key	Action
f	Cycle filter (All → Running → Failed → Pending → Completed)
s	Cycle sort (Status → Rule → Time)

Log Viewer

Key	Action
l / Enter	Open log viewer
F	Toggle follow mode
q / Escape	Close log viewer

General

Key	Action
?	Toggle help
r	Force refresh
q / Ctrl+C	Quit