diff --git a/tests/pipelines/cluster/.gitignore b/tests/pipelines/cluster/.gitignore
new file mode 100644
index 0000000..6bf305c
--- /dev/null
+++ b/tests/pipelines/cluster/.gitignore
@@ -0,0 +1,9 @@
+# Snakemake outputs
+results/
+logs/
+.snakemake/
+
+# Cluster job outputs
+slurm-*.out
+*.o*
+*.e*
diff --git a/tests/pipelines/cluster/Snakefile b/tests/pipelines/cluster/Snakefile
new file mode 100644
index 0000000..58eaa61
--- /dev/null
+++ b/tests/pipelines/cluster/Snakefile
@@ -0,0 +1,277 @@
+# Cluster test pipeline for charmer development
+# Designed to create many pending jobs and demonstrate failure handling
+#
+# DAG Structure (~76 jobs):
+#   process_sample (12) -> align_sample (12) -> call_variants (48)
+#                                                      |
+#                                              merge_sample_variants (12)
+#                                                      |
+#                                              group_analysis (2)
+#                                                      |
+#                                              final_merge (1)
+#                                                      |
+#                                              generate_report (1)
+
+configfile: "config/config.yaml"
+
+# Load samples configuration
+import yaml
+with open(config["samples_file"]) as f:
+    samples_config = yaml.safe_load(f)
+
+SAMPLES = list(samples_config["samples"].keys())
+CHROMOSOMES = config["chromosomes"]
+GROUPS = config["groups"]
+DELAYS = config["delays"]
+
+# Helper to get sample metadata
+def get_sample_meta(sample, key, default=None):
+    return samples_config["samples"].get(sample, {}).get(key, default)
+
+# Get samples that should succeed (no fail_at defined)
+SUCCESSFUL_SAMPLES = [s for s in SAMPLES if get_sample_meta(s, "fail_at") is None]
+
+# Get samples by group (excluding failure group)
+def get_samples_by_group(group):
+    return [s for s in SAMPLES
+            if get_sample_meta(s, "group") == group
+            and get_sample_meta(s, "fail_at") is None]
+
+rule all:
+    input:
+        "results/final_report.txt"
+
+rule process_sample:
+    """Initial sample processing - first step for all samples."""
+    output:
+        "results/processed/{sample}.txt"
+    params:
+        delay=DELAYS["process"],
+        fail_at=lambda wc: get_sample_meta(wc.sample, "fail_at"),
+        exit_code=lambda wc: get_sample_meta(wc.sample, "exit_code", 1)
+    threads: 1
+    resources:
+        mem_mb=2000,
+        runtime=10
+    log:
+        "logs/process_sample/{sample}.log"
+    shell:
+        """
+        exec > {log} 2>&1
+        echo "Starting processing for {wildcards.sample}..."
+        echo "INFO: Initializing sample processing pipeline"
+        echo "INFO: Checking input data integrity"
+
+        # Check if this sample should fail at this stage
+        if [ "{params.fail_at}" = "process" ]; then
+            echo "ERROR: Data validation failed for {wildcards.sample}"
+            echo "ERROR: Input file appears corrupted or malformed"
+            echo "ERROR: Cannot proceed with processing"
+            sleep 5
+            exit {params.exit_code}
+        fi
+
+        sleep {params.delay}
+        echo "INFO: Sample {wildcards.sample} processed successfully"
+        echo "Processed: {wildcards.sample}" > {output}
+        """
+
+rule align_sample:
+    """Alignment step - depends on processing."""
+    input:
+        "results/processed/{sample}.txt"
+    output:
+        "results/aligned/{sample}.bam"
+    params:
+        delay=DELAYS["align"],
+        fail_at=lambda wc: get_sample_meta(wc.sample, "fail_at"),
+        exit_code=lambda wc: get_sample_meta(wc.sample, "exit_code", 1)
+    threads: 2
+    resources:
+        mem_mb=4000,
+        runtime=15
+    log:
+        "logs/align_sample/{sample}.log"
+    shell:
+        """
+        exec > {log} 2>&1
+        echo "Starting alignment for {wildcards.sample}..."
+        echo "INFO: Loading reference genome"
+        sleep 5
+        echo "INFO: Indexing reference"
+        sleep 3
+        echo "INFO: Running aligner on {wildcards.sample}"
+
+        # Check if this sample should fail at this stage
+        if [ "{params.fail_at}" = "align" ]; then
+            echo "ERROR: Out of memory while aligning {wildcards.sample}"
+            echo "ERROR: Process killed by OOM killer"
+            echo "ERROR: Peak memory usage: 32.5 GB (limit: 16 GB)"
+            echo "ERROR: Consider increasing memory allocation"
+            sleep 2
+            exit {params.exit_code}
+        fi
+
+        sleep {params.delay}
+        echo "INFO: Alignment complete for {wildcards.sample}"
+        echo "INFO: Mapped reads: 45,234,567"
+        echo "INFO: Unmapped reads: 1,234,567"
+        echo "Aligned: {wildcards.sample}" > {output}
+        """
+
+rule call_variants:
+    """Variant calling per chromosome - creates fan-out pattern."""
+    input:
+        bam="results/aligned/{sample}.bam"
+    output:
+        vcf="results/variants/{sample}_{chrom}.vcf"
+    params:
+        delay=DELAYS["variants"],
+        fail_at=lambda wc: get_sample_meta(wc.sample, "fail_at"),
+        exit_code=lambda wc: get_sample_meta(wc.sample, "exit_code", 1)
+    threads: 2
+    resources:
+        mem_mb=4000,
+        runtime=20
+    log:
+        "logs/call_variants/{sample}_{chrom}.log"
+    shell:
+        """
+        exec > {log} 2>&1
+        echo "Starting variant calling for {wildcards.sample} on {wildcards.chrom}..."
+        echo "INFO: Loading BAM file"
+        sleep 3
+        echo "INFO: Scanning {wildcards.chrom} for variants"
+
+        # Check if this sample should fail at this stage
+        if [ "{params.fail_at}" = "call_variants" ]; then
+            echo "ERROR: Variant calling timed out for {wildcards.sample} on {wildcards.chrom}"
+            echo "ERROR: Wall clock limit exceeded"
+            echo "ERROR: Job ran for 3600 seconds (limit: 1800 seconds)"
+            sleep 2
+            exit {params.exit_code}
+        fi
+
+        sleep {params.delay}
+        echo "INFO: Found 12,345 variants on {wildcards.chrom}"
+        echo "INFO: SNPs: 10,234  Indels: 2,111"
+        echo "Variants: {wildcards.sample} {wildcards.chrom}" > {output.vcf}
+        """
+
+rule merge_sample_variants:
+    """Merge variants per sample across chromosomes - fan-in pattern."""
+    input:
+        expand("results/variants/{{sample}}_{chrom}.vcf", chrom=CHROMOSOMES)
+    output:
+        "results/merged/{sample}_merged.vcf"
+    params:
+        delay=DELAYS["merge"],
+        fail_at=lambda wc: get_sample_meta(wc.sample, "fail_at"),
+        exit_code=lambda wc: get_sample_meta(wc.sample, "exit_code", 1)
+    threads: 1
+    resources:
+        mem_mb=2000,
+        runtime=10
+    log:
+        "logs/merge_sample/{sample}.log"
+    shell:
+        """
+        exec > {log} 2>&1
+        echo "Starting variant merge for {wildcards.sample}..."
+        echo "INFO: Merging VCF files from {CHROMOSOMES}"
+
+        # Check if this sample should fail at this stage
+        if [ "{params.fail_at}" = "merge" ]; then
+            echo "ERROR: Segmentation fault while merging {wildcards.sample}"
+            echo "ERROR: Memory corruption detected at 0x7fff5fbff8c0"
+            echo "ERROR: Stack trace:"
+            echo "ERROR:   #0 merge_vcf_records() at vcfmerge.c:234"
+            echo "ERROR:   #1 main() at vcfmerge.c:567"
+            sleep 2
+            exit {params.exit_code}
+        fi
+
+        sleep {params.delay}
+        cat {input} > {output}
+        echo "INFO: Merge complete for {wildcards.sample}"
+        echo "INFO: Total variants: 49,380"
+        """
+
+rule group_analysis:
+    """Per-group analysis - aggregates samples by group."""
+    input:
+        lambda wc: expand("results/merged/{sample}_merged.vcf",
+                          sample=get_samples_by_group(wc.group))
+    output:
+        "results/groups/{group}_analysis.txt"
+    params:
+        delay=DELAYS["group_analysis"]
+    threads: 2
+    resources:
+        mem_mb=4000,
+        runtime=15
+    log:
+        "logs/group_analysis/{group}.log"
+    shell:
+        """
+        exec > {log} 2>&1
+        echo "Starting group analysis for {wildcards.group}..."
+        echo "INFO: Aggregating samples in group"
+        echo "INFO: Input samples: {input}"
+        sleep {params.delay}
+        echo "Group {wildcards.group} analysis complete" > {output}
+        echo "INFO: Analysis complete for {wildcards.group}"
+        """
+
+rule final_merge:
+    """Final merge of all group analyses."""
+    input:
+        expand("results/groups/{group}_analysis.txt", group=GROUPS)
+    output:
+        "results/final_analysis.txt"
+    params:
+        delay=DELAYS["final_merge"]
+    threads: 1
+    resources:
+        mem_mb=2000,
+        runtime=10
+    log:
+        "logs/final_merge.log"
+    shell:
+        """
+        exec > {log} 2>&1
+        echo "Starting final merge of all groups..."
+        echo "INFO: Combining group analyses"
+        sleep {params.delay}
+        cat {input} > {output}
+        echo "INFO: Final merge complete"
+        """
+
+rule generate_report:
+    """Generate final pipeline report."""
+    input:
+        analysis="results/final_analysis.txt",
+        merged=expand("results/merged/{sample}_merged.vcf", sample=SUCCESSFUL_SAMPLES)
+    output:
+        "results/final_report.txt"
+    params:
+        delay=DELAYS["report"]
+    threads: 1
+    resources:
+        mem_mb=1000,
+        runtime=5
+    log:
+        "logs/generate_report.log"
+    shell:
+        """
+        exec > {log} 2>&1
+        echo "Generating final report..."
+        echo "INFO: Collecting pipeline statistics"
+        sleep {params.delay}
+        echo "=== Pipeline Complete ===" > {output}
+        echo "Successful samples: {SUCCESSFUL_SAMPLES}" >> {output}
+        echo "Groups analyzed: {GROUPS}" >> {output}
+        echo "Chromosomes: {CHROMOSOMES}" >> {output}
+        date >> {output}
+        echo "INFO: Report generated successfully"
+        """
diff --git a/tests/pipelines/cluster/cluster/lsf/config.yaml b/tests/pipelines/cluster/cluster/lsf/config.yaml
new file mode 100644
index 0000000..6b67c5b
--- /dev/null
+++ b/tests/pipelines/cluster/cluster/lsf/config.yaml
@@ -0,0 +1,48 @@
+# Snakemake LSF Executor Profile Configuration
+# =============================================
+# This profile configures Snakemake to submit jobs to LSF clusters
+# Usage: snakemake --profile cluster/lsf
+
+# Executor settings
+executor: lsf
+jobs: 50                       # Maximum concurrent jobs
+latency-wait: 15               # Wait time for output files (seconds)
+
+# Default resources for all rules
+default-resources:
+  - "runtime=30"
+  - "mem_mb=4000"
+  - "lsf_queue=rna"
+  - "lsf_project=charmer-test"
+  - 'lsf_extra=""'
+
+# Rule-specific resource overrides
+set-resources:
+  - process_sample:runtime=10
+  - process_sample:mem_mb=2000
+
+  - align_sample:runtime=15
+  - align_sample:mem_mb=4000
+
+  - call_variants:runtime=20
+  - call_variants:mem_mb=4000
+
+  - merge_sample_variants:runtime=10
+  - merge_sample_variants:mem_mb=2000
+
+  - group_analysis:runtime=15
+  - group_analysis:mem_mb=4000
+
+  - final_merge:runtime=10
+  - final_merge:mem_mb=2000
+
+  - generate_report:runtime=5
+  - generate_report:mem_mb=1000
+
+# Behavior settings
+rerun-incomplete: true
+keep-going: true
+
+# Output settings
+printshellcmds: true
+show-failed-logs: true
diff --git a/tests/pipelines/cluster/cluster/slurm/config.yaml b/tests/pipelines/cluster/cluster/slurm/config.yaml
new file mode 100644
index 0000000..280c7da
--- /dev/null
+++ b/tests/pipelines/cluster/cluster/slurm/config.yaml
@@ -0,0 +1,63 @@
+# Snakemake SLURM Executor Profile Configuration
+# ================================================
+# This profile configures Snakemake to submit jobs to SLURM clusters
+# Usage: snakemake --profile cluster/slurm
+
+# Executor settings
+executor: slurm
+jobs: 50                       # Maximum concurrent jobs
+latency-wait: 60               # Wait time for output files (seconds)
+
+# Default resources for all rules
+default-resources:
+  slurm_partition: "amilan"    # Default CPU partition (Alpine)
+  slurm_account: "amc-general" # Alpine allocation account
+  slurm_qos: "normal"          # Default QoS
+  runtime: 30                  # Default walltime in minutes
+  mem_mb: 4000                 # Default memory in MB (4GB)
+  cpus_per_task: 1             # Default CPUs per task
+
+# Rule-specific resource overrides
+set-resources:
+  process_sample:
+    runtime: 10
+    mem_mb: 2000
+    cpus_per_task: 1
+
+  align_sample:
+    runtime: 15
+    mem_mb: 4000
+    cpus_per_task: 2
+
+  call_variants:
+    runtime: 20
+    mem_mb: 4000
+    cpus_per_task: 2
+
+  merge_sample_variants:
+    runtime: 10
+    mem_mb: 2000
+    cpus_per_task: 1
+
+  group_analysis:
+    runtime: 15
+    mem_mb: 4000
+    cpus_per_task: 2
+
+  final_merge:
+    runtime: 10
+    mem_mb: 2000
+    cpus_per_task: 1
+
+  generate_report:
+    runtime: 5
+    mem_mb: 1000
+    cpus_per_task: 1
+
+# Behavior settings
+rerun-incomplete: true
+keep-going: true
+
+# Output settings
+printshellcmds: true
+show-failed-logs: true
diff --git a/tests/pipelines/cluster/config/config.yaml b/tests/pipelines/cluster/config/config.yaml
new file mode 100644
index 0000000..760f9f5
--- /dev/null
+++ b/tests/pipelines/cluster/config/config.yaml
@@ -0,0 +1,27 @@
+# Pipeline configuration for cluster test pipeline
+
+project: "charmer-test"
+samples_file: "config/samples.yaml"
+output_dir: "results"
+
+# Chromosomes for variant calling (creates fan-out)
+chromosomes:
+  - chr1
+  - chr2
+  - chr3
+  - chr4
+
+# Groups for analysis
+groups:
+  - control
+  - treatment
+
+# Job timing (seconds) - short for testing
+delays:
+  process: 30
+  align: 60
+  variants: 45
+  merge: 20
+  group_analysis: 30
+  final_merge: 15
+  report: 10
diff --git a/tests/pipelines/cluster/config/samples.yaml b/tests/pipelines/cluster/config/samples.yaml
new file mode 100644
index 0000000..8f866d3
--- /dev/null
+++ b/tests/pipelines/cluster/config/samples.yaml
@@ -0,0 +1,62 @@
+# Sample configuration for cluster test pipeline
+# 12 samples: 8 successful + 4 designed to fail at different stages
+
+samples:
+  # Control group - 4 samples
+  ctrl-rep1:
+    group: control
+    replicate: 1
+
+  ctrl-rep2:
+    group: control
+    replicate: 2
+
+  ctrl-rep3:
+    group: control
+    replicate: 3
+
+  ctrl-rep4:
+    group: control
+    replicate: 4
+
+  # Treatment group - 4 samples
+  treat-rep1:
+    group: treatment
+    replicate: 1
+
+  treat-rep2:
+    group: treatment
+    replicate: 2
+
+  treat-rep3:
+    group: treatment
+    replicate: 3
+
+  treat-rep4:
+    group: treatment
+    replicate: 4
+
+  # Samples designed to FAIL with different errors
+  fail-oom:
+    group: failure
+    replicate: 1
+    fail_at: align           # Fails during alignment
+    exit_code: 137           # OOM kill signal
+
+  fail-timeout:
+    group: failure
+    replicate: 2
+    fail_at: call_variants   # Fails during variant calling
+    exit_code: 124           # Timeout signal
+
+  fail-error:
+    group: failure
+    replicate: 3
+    fail_at: process         # Fails during initial processing
+    exit_code: 1             # Generic error
+
+  fail-segfault:
+    group: failure
+    replicate: 4
+    fail_at: merge           # Fails during merge
+    exit_code: 139           # Segfault signal