Updated environment and formatted .smk files (#18)

environment.yml

@@ -9,4 +9,5 @@ dependencies:
   - pytest==8.2.1
   - pillow==10.3.0
   - pdf2image==1.17.0 
-  - samtools==1.20
+  - samtools==1.20
+  - snakefmt==0.10.2

workflow/rules/cnv.smk

@@ -1,185 +1,221 @@
 rule cnvkit_target_coverage:
     input:
-        bam=os.path.join(config['outdir'], 'preprocessing', '{sample}.sorted.bam'),
-        bai=os.path.join(config['outdir'], 'preprocessing', '{sample}.sorted.bam.bai'),
-        target_bed=config['ref']['target_bed'] 
+        bam=os.path.join(config["outdir"], "preprocessing", "{sample}.sorted.bam"),
+        bai=os.path.join(config["outdir"], "preprocessing", "{sample}.sorted.bam.bai"),
+        target_bed=config["ref"]["target_bed"],
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.targetcoverage.cnn')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.targetcoverage.cnn"),
     params:
-        extra=config['params']['cnvkit']['target_coverage']['extra']
+        extra=config["params"]["cnvkit"]["target_coverage"]["extra"],
     threads: 8
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_target_coverage', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_target_coverage", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py coverage {input.bam} {input.target_bed} -o {output} -p {threads} {params.extra} > {log} 2>&1"
 
+
 rule cnvkit_antitarget_coverage:
     input:
-        bam=os.path.join(config['outdir'], 'preprocessing', '{sample}.sorted.bam'),
-        bai=os.path.join(config['outdir'], 'preprocessing', '{sample}.sorted.bam.bai'),
-        antitarget_bed=config['ref']['antitarget_bed']
+        bam=os.path.join(config["outdir"], "preprocessing", "{sample}.sorted.bam"),
+        bai=os.path.join(config["outdir"], "preprocessing", "{sample}.sorted.bam.bai"),
+        antitarget_bed=config["ref"]["antitarget_bed"],
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.antitargetcoverage.cnn')
+        os.path.join(
+            config["outdir"], "cnv", "{sample}", "{sample}.antitargetcoverage.cnn"
+        ),
     params:
-        extra=config['params']['cnvkit']['antitarget_coverage']['extra']
+        extra=config["params"]["cnvkit"]["antitarget_coverage"]["extra"],
     threads: 8
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_antitarget_coverage', '{sample}.log')
+        os.path.join(
+            config["outdir"], "logs", "cnvkit_antitarget_coverage", "{sample}.log"
+        ),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py coverage {input.bam} {input.antitarget_bed} -o {output} -p {threads} {params.extra} > {log} 2>&1"
 
+
 rule cnvkit_reference:
     input:
-        target=collect(os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.targetcoverage.cnn'), sample=SAMPLES.index),
-        antitarget=collect(os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.antitargetcoverage.cnn'), sample=SAMPLES.index),
-        ref=config['ref']['genome']
+        target=collect(
+            os.path.join(
+                config["outdir"], "cnv", "{sample}", "{sample}.targetcoverage.cnn"
+            ),
+            sample=SAMPLES.index,
+        ),
+        antitarget=collect(
+            os.path.join(
+                config["outdir"], "cnv", "{sample}", "{sample}.antitargetcoverage.cnn"
+            ),
+            sample=SAMPLES.index,
+        ),
+        ref=config["ref"]["genome"],
     output:
-        os.path.join(config['outdir'], 'cnv', 'reference.cnn')
+        os.path.join(config["outdir"], "cnv", "reference.cnn"),
     params:
-        extra=config['params']['cnvkit']['reference']['extra']
+        extra=config["params"]["cnvkit"]["reference"]["extra"],
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_reference.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_reference.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py reference {input.target} {input.antitarget} --fasta {input.ref} -o {output} > {log} 2>&1"
 
+
 rule cnvkit_fix:
     input:
-        target=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.targetcoverage.cnn'),
-        antitarget=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.antitargetcoverage.cnn'),
-        reference=os.path.join(config['outdir'], 'cnv', 'reference.cnn')
+        target=os.path.join(
+            config["outdir"], "cnv", "{sample}", "{sample}.targetcoverage.cnn"
+        ),
+        antitarget=os.path.join(
+            config["outdir"], "cnv", "{sample}", "{sample}.antitargetcoverage.cnn"
+        ),
+        reference=os.path.join(config["outdir"], "cnv", "reference.cnn"),
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cnr')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cnr"),
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_fix', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_fix", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py fix {input.target} {input.antitarget} {input.reference} -o {output} > {log} 2>&1"
 
+
 rule cnvkit_segment:
     input:
-        cnr=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cnr'),
-        vcf=get_vcf
+        cnr=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cnr"),
+        vcf=get_vcf,
     output:
-        temp(os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cns'))
+        temp(os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cns")),
     params:
-        extra=config['params']['cnvkit']['segment']['extra']
-    threads: 1 # Limited by HMM method
+        extra=config["params"]["cnvkit"]["segment"]["extra"],
+    threads: 1  # Limited by HMM method
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_segment', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_segment", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py segment -m hmm {input.cnr} -o {output} --vcf {input.vcf} -p {threads} > {log} 2>&1"
 
+
 rule cnvkit_call:
     input:
-        cns=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cns'),
-        vcf=get_vcf
+        cns=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cns"),
+        vcf=get_vcf,
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_call.cns')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_call.cns"),
     params:
-        ploidy=config['params']['cnvkit']['call']['ploidy']
+        ploidy=config["params"]["cnvkit"]["call"]["ploidy"],
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_call', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_call", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py call {input.cns} -o {output} -v {input.vcf} --ploidy {params.ploidy} > {log} 2>&1"
 
+
 rule cnvkit_bintest:
     input:
-        cnr=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cnr'),
-        call_cns=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_call.cns')
+        cnr=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cnr"),
+        call_cns=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_call.cns"),
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_bintest.tsv')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_bintest.tsv"),
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_bintest', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_bintest", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py bintest {input.cnr} -s {input.call_cns} --target -o {output} > {log} 2>&1"
 
+
 rule cnvkit_breaks:
     input:
-        cnr=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cnr'),
-        cns=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cns')
+        cnr=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cnr"),
+        cns=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cns"),
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_breaks.tsv')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_breaks.tsv"),
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_breaks', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_breaks", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py breaks {input.cnr} {input.cns} > {output} 2>&1"
 
+
 rule cnvkit_genemetrics:
     input:
-        cnr=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cnr'),
-        cns=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cns')
+        cnr=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cnr"),
+        cns=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cns"),
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_genemetrics.tsv')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_genemetrics.tsv"),
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_genemetrics', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_genemetrics", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py genemetrics {input.cnr} -s {input.cns} > {output} 2>&1"
 
+
 rule cnvkit_scatter_pdf:
     input:
-        cnr=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cnr'),
-        call_cns=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_call.cns'),
-        vcf=get_vcf
+        cnr=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cnr"),
+        call_cns=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_call.cns"),
+        vcf=get_vcf,
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_scatter.pdf')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_scatter.pdf"),
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_scatter_pdf', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_scatter_pdf", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py scatter {input.cnr} -s {input.call_cns} --y-min -2.5 -v {input.vcf} -o {output} > {log} 2>&1"
 
+
 rule cnvkit_scatter_png:
     input:
-        cnr=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cnr'),
-        call_cns=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_call.cns'),
-        vcf=get_vcf
+        cnr=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cnr"),
+        call_cns=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_call.cns"),
+        vcf=get_vcf,
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_scatter.png')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_scatter.png"),
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_scatter_png', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_scatter_png", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py scatter {input.cnr} -s {input.call_cns} --y-min -2.5 -v {input.vcf} -o {output} > {log} 2>&1"
 
+
 rule cnvkit_export_vcf:
     input:
-        call_cns=os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_call.cns')
+        call_cns=os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_call.cns"),
     output:
-        os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_cnv.vcf')
+        os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_cnv.vcf"),
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_export_vcf', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_export_vcf", "{sample}.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:
         "cnvkit.py export vcf {input.call_cns} -i {wildcards.sample} -o {output} > {log} 2>&1"
 
+
 rule cnvkit_metrics:
     input:
-        expand(os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}.cnr'), sample=SAMPLES.index),
-        expand(os.path.join(config['outdir'], 'cnv', '{sample}', '{sample}_call.cns'), sample=SAMPLES.index)
+        expand(
+            os.path.join(config["outdir"], "cnv", "{sample}", "{sample}.cnr"),
+            sample=SAMPLES.index,
+        ),
+        expand(
+            os.path.join(config["outdir"], "cnv", "{sample}", "{sample}_call.cns"),
+            sample=SAMPLES.index,
+        ),
     output:
-        os.path.join(config['outdir'], 'cnv', 'run_metrics.tsv')
+        os.path.join(config["outdir"], "cnv", "run_metrics.tsv"),
     log:
-        os.path.join(config['outdir'], 'logs', 'cnvkit_metrics.log')
+        os.path.join(config["outdir"], "logs", "cnvkit_metrics.log"),
     conda:
         "../envs/cnvkit.yaml"
     shell:

workflow/rules/common.smk

@@ -4,11 +4,14 @@ from snakemake.utils import min_version
 
 min_version("8.12.0")
 
+
 report: "../report/workflow.rst"
 
+
 ###### Config file and sample sheets #####
 configfile: "config/config.yaml"
 
+
 SAMPLES = pd.read_table(config["samples"]).set_index("sample", drop=False)
 
 snakedir = workflow.basedir
@@ -20,10 +23,12 @@ validate(SAMPLES, schema="../schemas/samplesheet.schema.yaml")
 
 ##### Helper functions #####
 
+
 def get_bam(wildcards):
     """Retrieve BAM file for a given sample."""
-    return SAMPLES.loc[wildcards.sample, 'bam_path']
+    return SAMPLES.loc[wildcards.sample, "bam_path"]
+
 
 def get_vcf(wildcards):
     """Retrieve VCF file for a given sample."""
-    return SAMPLES.loc[wildcards.sample, 'vcf_path']
+    return SAMPLES.loc[wildcards.sample, "vcf_path"]

workflow/rules/preprocessing.smk

@@ -1,24 +1,25 @@
 rule samtools_sort:
     input:
-       get_bam
+        get_bam,
     output:
-        os.path.join(config['outdir'], 'preprocessing', '{sample}.sorted.bam')
+        os.path.join(config["outdir"], "preprocessing", "{sample}.sorted.bam"),
     log:
-        os.path.join(config['outdir'], 'logs', 'samtools_sort', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "samtools_sort", "{sample}.log"),
     threads: 8
     conda:
         "../envs/samtools.yaml"
     shell:
         "samtools sort -@ {threads} {input} -o {output} > {log} 2>&1"
 
+
 rule samtools_index:
     input:
-        os.path.join(config['outdir'], 'preprocessing', '{sample}.sorted.bam')
+        os.path.join(config["outdir"], "preprocessing", "{sample}.sorted.bam"),
     output:
-        os.path.join(config['outdir'], 'preprocessing', '{sample}.sorted.bam.bai')
+        os.path.join(config["outdir"], "preprocessing", "{sample}.sorted.bam.bai"),
     log:
-        os.path.join(config['outdir'], 'logs', 'samtools_index', '{sample}.log')
+        os.path.join(config["outdir"], "logs", "samtools_index", "{sample}.log"),
     conda:
         "../envs/samtools.yaml"
     shell:
-        "samtools index {input} > {log} 2>&1"
+        "samtools index {input} > {log} 2>&1"