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feat: Add dedicated demo pipeline for VHS recordings
- Create tests/pipelines/demo with 12 samples, 9 rules - Staggered timing shows job accumulation and progression - Fan-out pattern (3 regions per sample) demonstrates dependency chains - Update demo.tape with longer recording showing Jobs/Rules views - Update generate.sh to use demo pipeline with 4 cores - Add clean-demo task to pixi.toml 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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‎docs/images/demo.gif‎

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‎docs/images/quickstart.gif‎

-22.9 KB
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‎docs/tapes/demo.tape‎

Lines changed: 53 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -15,40 +15,80 @@ Type "# charmer - Snakemake Pipeline Monitor"
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Enter
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Sleep 1s
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# Show help
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# Show help briefly
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Type "charmer --help"
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Enter
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Sleep 3s
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Sleep 2s
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# Clear and start the TUI
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Hide
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Type "clear"
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Enter
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Show
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# Start charmer with test data
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Type "charmer tests/pipelines/simple"
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# Start charmer with demo pipeline
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Type "charmer tests/pipelines/demo"
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Enter
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# Watch jobs accumulate
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Sleep 3s
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# Navigate down to see dependency chain highlighting
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Type "j"
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Sleep 400ms
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Type "j"
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Sleep 400ms
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Type "j"
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Sleep 400ms
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Type "j"
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Sleep 400ms
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Type "j"
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Sleep 1s
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# Watch more jobs complete
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Sleep 2s
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# Navigate through jobs
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# Go to bottom to see more jobs
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Type "G"
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Sleep 1.5s
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# Back to top
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Type "g"
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Sleep 1s
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# Switch to Rules view
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Type@100ms "Tab"
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Sleep 2s
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# Navigate rules
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Type "j"
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Sleep 500ms
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Type "j"
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Sleep 500ms
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Type "j"
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Sleep 500ms
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Sleep 1s
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# Show filtering
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Type "f"
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# Back to Jobs view
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Type@100ms "Tab"
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Sleep 1s
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# Filter to running jobs only
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Type "f"
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Sleep 1s
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Sleep 1.5s
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# Filter to completed
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Type "f"
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Sleep 1.5s
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# Back to all jobs
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Type "f"
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Sleep 500ms
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Type "f"
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Sleep 1s
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# Show sorting
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# Change sort order
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Type "s"
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Sleep 1s
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Type "s"
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Sleep 1s
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Type "s"
@@ -60,12 +100,9 @@ Sleep 2s
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Type "?"
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Sleep 500ms
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# Navigate more
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Type "G"
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Sleep 1s
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Type "g"
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Sleep 1s
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# Final view of accumulating jobs
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Sleep 2s
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# Quit
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Type "q"
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Sleep 1s
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Sleep 500ms

‎docs/tapes/generate.sh‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,9 @@ cd "$ROOT_DIR"
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# Install charmer binary
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cargo install --path crates/charmer
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# Clean and start the test pipeline
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pixi run clean-test
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snakemake --cores 2 --snakefile tests/pipelines/simple/Snakefile --directory tests/pipelines/simple &
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# Clean and start the demo pipeline
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pixi run clean-demo
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snakemake --cores 4 --snakefile tests/pipelines/demo/Snakefile --directory tests/pipelines/demo &
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PIPELINE_PID=$!
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# Wait for jobs to register

‎docs/tapes/quickstart.tape‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ Type "# Start monitoring"
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Enter
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Sleep 500ms
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Type "charmer tests/pipelines/simple"
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Type "charmer tests/pipelines/demo"
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Enter
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Sleep 3s
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‎pixi.toml‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,10 @@ platforms = ["osx-arm64", "osx-64", "linux-64"]
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test-pipeline = "cd tests/pipelines/simple && snakemake --cores 2 --snakefile Snakefile"
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# Clean test pipeline outputs (including .snakemake metadata)
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clean-test = "cd tests/pipelines/simple && rm -rf results .snakemake"
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clean-test = "cd tests/pipelines/simple && rm -rf results logs .snakemake"
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# Clean demo pipeline outputs
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clean-demo = "cd tests/pipelines/demo && rm -rf results logs .snakemake"
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# Dry run to see what would be executed
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dry-run = "cd tests/pipelines/simple && snakemake --cores 2 --dry-run"

‎tests/pipelines/demo/.gitignore‎

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@@ -0,0 +1,3 @@
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results/
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logs/
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.snakemake/

‎tests/pipelines/demo/Snakefile‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,154 @@
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# Demo pipeline optimized for charmer VHS recordings
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# Designed to show: job accumulation, dependency chains, multiple rules
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SAMPLES = [f"sample{i}" for i in range(1, 13)] # 12 samples
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REGIONS = ["region_A", "region_B", "region_C"]
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rule all:
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input:
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"results/final_summary.txt"
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rule download:
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"""Download raw data - fast, runs first for all samples."""
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output:
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"results/raw/{sample}.fastq"
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params:
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delay = lambda wc: 2 + (hash(wc.sample) % 3) # 2-4 seconds, varies by sample
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log:
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"logs/download/{sample}.log"
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shell:
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"""
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exec > {log} 2>&1
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echo "Downloading {wildcards.sample}..."
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sleep {params.delay}
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echo "Downloaded" > {output}
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"""
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rule quality_check:
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"""QC step - depends on download."""
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input:
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"results/raw/{sample}.fastq"
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output:
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"results/qc/{sample}_qc.txt"
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params:
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delay = lambda wc: 3 + (hash(wc.sample) % 4) # 3-6 seconds
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log:
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"logs/qc/{sample}.log"
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shell:
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"""
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exec > {log} 2>&1
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echo "Running QC on {wildcards.sample}..."
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sleep {params.delay}
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echo "QC passed" > {output}
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"""
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rule align:
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"""Alignment - depends on QC, longer running."""
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input:
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fastq = "results/raw/{sample}.fastq",
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qc = "results/qc/{sample}_qc.txt"
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output:
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"results/aligned/{sample}.bam"
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params:
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delay = lambda wc: 5 + (hash(wc.sample) % 5) # 5-9 seconds
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log:
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"logs/align/{sample}.log"
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shell:
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"""
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exec > {log} 2>&1
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echo "Aligning {wildcards.sample}..."
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sleep {params.delay}
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echo "Aligned" > {output}
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"""
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rule call_peaks:
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"""Peak calling per region - creates fan-out from alignment."""
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input:
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"results/aligned/{sample}.bam"
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output:
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"results/peaks/{sample}_{region}.bed"
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params:
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delay = lambda wc: 4 + (hash(wc.sample + wc.region) % 4) # 4-7 seconds
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log:
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"logs/peaks/{sample}_{region}.log"
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shell:
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"""
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exec > {log} 2>&1
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echo "Calling peaks for {wildcards.sample} in {wildcards.region}..."
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sleep {params.delay}
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echo "Peaks found" > {output}
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"""
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rule merge_peaks:
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"""Merge peaks per sample - depends on all regions."""
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input:
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expand("results/peaks/{{sample}}_{region}.bed", region=REGIONS)
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output:
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"results/merged/{sample}_peaks.bed"
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params:
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delay = 3
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log:
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"logs/merge/{sample}.log"
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shell:
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"""
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exec > {log} 2>&1
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echo "Merging peaks for {wildcards.sample}..."
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sleep {params.delay}
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cat {input} > {output}
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"""
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rule annotate:
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"""Annotate merged peaks."""
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input:
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"results/merged/{sample}_peaks.bed"
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output:
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"results/annotated/{sample}_annotated.txt"
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params:
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delay = 4
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log:
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"logs/annotate/{sample}.log"
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shell:
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"""
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exec > {log} 2>&1
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echo "Annotating {wildcards.sample}..."
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sleep {params.delay}
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echo "Annotated" > {output}
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"""
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rule sample_report:
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"""Per-sample report - end of chain per sample."""
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input:
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annotated = "results/annotated/{sample}_annotated.txt",
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bam = "results/aligned/{sample}.bam"
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output:
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"results/reports/{sample}_report.txt"
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params:
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delay = 2
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log:
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"logs/report/{sample}.log"
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shell:
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"""
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exec > {log} 2>&1
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echo "Generating report for {wildcards.sample}..."
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sleep {params.delay}
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echo "Report for {wildcards.sample}" > {output}
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"""
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rule final_summary:
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"""Final summary - depends on all sample reports."""
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input:
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expand("results/reports/{sample}_report.txt", sample=SAMPLES)
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output:
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"results/final_summary.txt"
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params:
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delay = 3
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log:
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"logs/final_summary.log"
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shell:
148+
"""
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exec > {log} 2>&1
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echo "Creating final summary..."
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sleep {params.delay}
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echo "Pipeline complete" > {output}
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cat {input} >> {output}
154+
"""

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