test.smk

# =============================================================================
# Snakefile — comprehensive feature test for Snakemake highlighting
# Minimal comments; lines marked `# ERROR:` are intentionally invalid.
# =============================================================================
# ---------- Top-level Python ----------
if True: forbidden # ERROR: no text allowed after block opener
 a = 1
else: forbidden # ERROR: same
 a = 0
config = {
 "method": "B",
 "samples": ["S1", "S2"],
 "ref": "ref/genome.fa",
 "gtf": "ref/genes.gtf",
 "threads_default": 4,
 "work": "work",
 "adapters": {"fwd": "AGATCGGAAGAGC", "rev": "AGATCGGAAGAGC"}
}
SAMPLES = config["samples"]
def fq(sample, mate):
 return f"raw/{sample}_R{mate}.fastq.gz"
# ---------- Global Snakemake directives ----------
workdir: config["work"]
localrules: all, qc_fastqc
ruleorder: sort_index> align
report: "report/report.html"
envvars: "LD_LIBRARY_PATH", "OMP_NUM_THREADS"
wildcard_constraints:
 sample = r"[A-Za-z0-9_]+"
include: "extras.smk"
container: "docker://ubuntu:22.04"
conda: "envs/global.yml"
containerized:
# Legacy/compat directives still recognized in old workflows
moduleinclude: "legacy/tools.smk" # legacy include for modules
# deprecated (kept for legacy)
subworkflow oldwf: something #ERROR: nothing allowed after colon
 workdir: "oldwf"
 snakefile: "workflow/Snakefile"
 input: # ERROR: `input` directive not allowed in subworkflows
# ---------- Modules and use rule ----------
module asm: something #ERROR: nothing allowed after colon
 snakefile: "modules/assembly.smk"
 config: "modules/assembly.yaml"
 input: "test" # ERROR: `input` directive not allowed in modules
# Reuse a rule from the module; inside `with:` we use regular rule directives
use rule assemble as assemble_mod with: something #ERROR: nothing allowed after colon
 snakefile: # ERROR `snakefile` directive not allowed in rules
 threads: 8
 params:
 mode = "quick"
 message:
 "Assembling {wildcards.sample} (module override)"
 # wrong directive (kept to test error handling inside a use-body)
 outpt: "SHOULD-NOT-BE-HERE" # ERROR: typo
# ---------- INTENTIONAL TOP-LEVEL ERRORS ----------
workdirr: "typo/dir" # ERROR: unknown top-level keyword
snakefile: "top/level.smk" # ERROR: only valid inside module/subworkflow
# ---------- Pipeline ----------
rule all:
 input:
 expand("results/{sample}/summary.txt", sample=SAMPLES)
rule qc_fastqc:
 input:
 r1 = lambda wc: fq(wc.sample, 1),
 r2 = lambda wc: fq(wc.sample, 2),
 output:
 html = "qc/{sample}_fastqc.html",
 zip = "qc/{sample}_fastqc.zip",
 threads: 2
 resources:
 mem_mb = 1024
 log:
 "log/fastqc_{sample}.log"
 params:
 extra = "--nogroup"
 shell:
 """
 fastqc -t {threads}{params.extra} -o qc {input.r1}{input.r2}> {log} 2>&1
 """
rule trim_cutadapt:
 input:
 r1 = lambda wc: fq(wc.sample, 1),
 r2 = lambda wc: fq(wc.sample, 2),
 output:
 r1 = "trim/{sample}_R1.fastq.gz", # `sample`: wildcard
 r2 = "trim/{sample}_R2.fastq.gz",
 report = f"{report_dir}/{{sample}}" # `report_dir`: f-string interpolation, `sample`: wildcard
 params:
 a = config["adapters"]["fwd"],
 A = config["adapters"]["rev"],
 threads: 8
 conda:
 "envs/cutadapt.yml"
 log:
 "log/cutadapt_{sample}.log"
 shell:
 """
 cutadapt -j {threads} -a {params.a} -A {params.A} \
 -o {output.r1} -p {output.r2}{input.r1}{input.r2}> {log} 2>&1
 """
# Example of wrapper usage (version string illustrative)
rule align:
 input:
 r1 = "trim/{sample}_R1.fastq.gz",
 r2 = "trim/{sample}_R2.fastq.gz",
 ref = config["ref"],
 output:
 bam = "map/{sample}.unsorted.bam",
 threads: 12
 resources:
 mem_mb = 8000
 params:
 # BWA-MEM2 example options
 extra = "-M"
 log:
 "log/align_{sample}.log"
 wrapper:
 "0.90.0/bio/bwa/mem2"
 shell:
 "bwa-mem2 mem -t {threads}{params.extra}{input.ref}{input.r1}{input.r2} | samtools view -bS -> {output.bam} 2> {log}"
rule sort_index:
 input:
 "map/{sample}.unsorted.bam"
 output:
 bam = "map/{sample}.bam",
 bai = "map/{sample}.bam.bai",
 threads: 6
 resources:
 mem_mb = 4000
 envmodules:
 "samtools/1.16"
 shadow:
 "minimal"
 shell:
 """
 samtools sort -@ {threads} -o {output.bam}{input}
 samtools index -@ {threads}{output.bam}
 """
rule quantify:
 input:
 bam = "map/{sample}.bam",
 bai = "map/{sample}.bam.bai",
 gtf = config["gtf"],
 output:
 counts = "counts/{sample}.txt",
 threads: 4
 group:
 "counting"
 priority:
 50
 params:
 feature_type = "exon",
 id_attr = "gene_id",
 shell:
 """
 featureCounts -T {threads} -a {input.gtf} -t {params.feature_type} -g {params.id_attr} \
 -o {output.counts}{input.bam}
 """
# Example of script & notebook directives
rule plot_qc:
 input:
 "qc/{sample}_fastqc.zip"
 output:
 "plots/{sample}_qc.png"
 script:
 "scripts/plot_qc.py" # not executed; present to test directive
rule explore_notebook:
 input:
 "counts/{sample}.txt"
 output:
 "notebooks/{sample}_eda.ipynb"
 notebook:
 "notebooks/template.ipynb"
# Example of per-rule container / cache / benchmark / message / name / version (legacy)
rule summarize:
 input:
 bam = "map/{sample}.bam",
 counts = "counts/{sample}.txt"
 output:
 txt = "results/{sample}/summary.txt"
 params:
 tag = "{sample}" # wildcard should highlight distinctly
 message:
 "Summarizing {wildcards.sample}"
 name:
 "summarize_{sample}"
 benchmark:
 "benchmark/summarize_{sample}.tsv"
 cache:
 "permissive"
 container:
 "docker://python:3.11"
 version: "1.0" # legacy directive
 threads: 2
 resources:
 mem_mb = 512
 log:
 "log/summarize_{sample}.log"
 run:
 # simple Python run block
 import json
 meta = {
 "sample": wildcards.sample,
 "bam": input.bam,
 "counts": input.counts,
 "tag": params.tag,
 }
 # write a tiny summary
 import os
 os.makedirs(os.path.dirname(output.txt), exist_ok=True)
 with open(output.txt, "w") as fh:
 fh.write(json.dumps(meta, indent=2) + "\n")
# ---------- More intentional errors inside a rule body ----------
if config["method"] == "A":
 
 rule bad_header_examples_A:
 input:
 "map/{sample}.bam"
 outpt: # ERROR: unknown directive
 "nowhere.txt"
 foo: # ERROR: unknown directive
 "bar"
 shell:
 "true"
else:
 rule bad_header_examples_B:
 input:
 "map/{sample}.bam"
 output: # ERROR: unknown directive
 "nowhere.txt"
 foo: # ERROR: unknown directive
 "bar"
 shell:
 "true"
# ---------- Using the module rule ----------
rule assemble_via_module:
 input:
 "trim/{sample}_R1.fastq.gz",
 "trim/{sample}_R2.fastq.gz",
 output:
 "assembly/{sample}/contigs.fa"
 threads: 8
 shell:
 "echo assembly> {output}"
# ---------- Default target redirection ----------
rule final_default:
 output:
 "FINAL.marker"
 default_target:
 True
 shell:
 "touch {output}"
 
rule: no text allowed here # ERROR: no text allowed after block opener
 input: "back_to_normal.txt"