feat: GATK Meta-wrapper update to follow pathvars

meta/bio/gatk_mutect2_calling/meta.yaml

@@ -27,3 +27,17 @@ description: >
     +----------------+---------------------------+-------------------------------------------------------------+
 authors:
   - Thibault Dayris
+pathvars:
+  default:
+    - results
+    - resources
+    - logs
+  custom:
+    per: Pattern for sample identifiers, e.g. ``"{sample}"``
+    genome_sequence: Path to FASTA file with genome sequence
+    genome_sequence_index: Path to FAI file with genome sequence index
+    genome_dict: Path to DICT file with genome sequence dictionary
+    bed_intervals: Path to BED file with genome intervals
+    known_variants: Path to gzipped VCF file containing known variants
+    known_variants_tbi: Path to TBI index corresponding to known variants
+    bam_file: Path/Pattern to aligned reads (SAM/BAM/CRAM)

meta/bio/gatk_mutect2_calling/meta_wrapper.smk

@@ -1,13 +1,13 @@
 rule create_dict:
     input:
-        "genome.fasta",
+        "<genome_sequence>",
     output:
-        "genome.dict",
+        "<genome_dict>",
     threads: 1
     resources:
         mem_mb=1024,
     log:
-        "logs/picard/create_dict.log",
+        "<logs>/picard/create_dict.log",
     params:
         extra="",
     wrapper:
@@ -16,11 +16,11 @@ rule create_dict:
 
 rule samtools_index:
     input:
-        "genome.fasta",
+        "<genome_sequence>",
     output:
-        "genome.fasta.fai",
+        "<genome_sequence_index>",
     log:
-        "logs/genome_index.log",
+        "<logs>/genome_index.log",
     params:
         extra="",  # optional params string
     wrapper:
@@ -29,14 +29,14 @@ rule samtools_index:
 
 rule picard_replace_read_groups:
     input:
-        "mapped/{sample}.bam",
+        "<bam_file>",
     output:
-        "picard/{sample}.bam",
+        "<results>/picard/<per>.bam",
     threads: 1
     resources:
         mem_mb=1024,
     log:
-        "logs/picard/replace_rg/{sample}.log",
+        "<logs>/picard/replace_rg/<per>.log",
     params:
         # Required for GATK
         extra="--RGLB lib1 --RGPL illumina --RGPU {sample} --RGSM {sample}",
@@ -46,12 +46,12 @@ rule picard_replace_read_groups:
 
 rule sambamba_index_picard_bam:
     input:
-        "picard/{sample}.bam",
+        "<results>/picard/<per>.bam",
     output:
-        "picard/{sample}.bam.bai",
+        "<results>/picard/<per>.bam.bai",
     threads: 1
     log:
-        "logs/sambamba/index/{sample}.log",
+        "<logs>/sambamba/index/<per>.log",
     params:
         extra="",
     wrapper:
@@ -60,57 +60,57 @@ rule sambamba_index_picard_bam:
 
 rule mutect2_call:
     input:
-        fasta="genome.fasta",
-        fasta_dict="genome.dict",
-        fasta_fai="genome.fasta.fai",
-        map="picard/{sample}.bam",
-        map_idx="picard/{sample}.bam.bai",
-        intervals="regions.bed",
+        fasta="<genome_sequence>",
+        fasta_dict="<genome_dict>",
+        fasta_fai="<genome_sequence_index>",
+        map="<results>/picard/<per>.bam",
+        map_idx="<results>/picard/<per>.bam.bai",
+        intervals="<bed_intervals>",
     output:
-        vcf="variant/{sample}.vcf",
-        bam="variant/{sample}.bam",
-        f1r2="counts/{sample}.f1r2.tar.gz",
+        vcf="<results>/variant/<per>.vcf",
+        bam="<results>/variant/<per>.bam",
+        f1r2="<results>/counts/<per>.f1r2.tar.gz",
     threads: 1
     resources:
         mem_mb=1024,
     params:
         extra=" --tumor-sample {sample} ",
     log:
-        "logs/mutect/{sample}.log",
+        "<logs>/mutect/<per>.log",
     wrapper:
         "master/bio/gatk/mutect"
 
 
 rule gatk_get_pileup_summaries:
     input:
-        bam="picard/{sample}.bam",
-        bai="picard/{sample}.bam.bai",
-        variants="known.vcf.gz",
-        variants_tbi="known.vcf.gz.tbi",
-        intervals="regions.bed",
+        bam="<results>/picard/<per>.bam",
+        bai="<results>/picard/<per>.bam.bai",
+        variants="<known_variants>",
+        variants_tbi="<known_variants_tbi>",
+        intervals="<bed_intervals>",
     output:
-        temp("summaries/{sample}.table"),
+        temp("<results>/summaries/<per>.table"),
     threads: 1
     resources:
         mem_mb=1024,
     params:
         extra="",
     log:
-        "logs/summary/{sample}.log",
+        "<logs>/summary/<per>.log",
     wrapper:
         "master/bio/gatk/getpileupsummaries"
 
 
 rule gatk_calculate_contamination:
     input:
-        tumor="summaries/{sample}.table",
+        tumor="<results>/summaries/<per>.table",
     output:
-        temp("contamination/{sample}.pileups.table"),
+        temp("<results>/contamination/<per>.pileups.table"),
     threads: 1
     resources:
         mem_mb=1024,
     log:
-        "logs/contamination/{sample}.log",
+        "<logs>/contamination/<per>.log",
     params:
         extra="",
     wrapper:
@@ -119,38 +119,38 @@ rule gatk_calculate_contamination:
 
 rule gatk_learn_read_orientation_model:
     input:
-        f1r2="counts/{sample}.f1r2.tar.gz",
+        f1r2="<results>/counts/<per>.f1r2.tar.gz",
     output:
-        temp("artifacts_prior/{sample}.tar.gz"),
+        temp("<results>/artifacts_prior/<per>.tar.gz"),
     threads: 1
     resources:
         mem_mb=1024,
     params:
         extra="",
     log:
-        "logs/learnreadorientationbias/{sample}.log",
+        "<logs>/learnreadorientationbias/<per>.log",
     wrapper:
         "master/bio/gatk/learnreadorientationmodel"
 
 
 rule filter_mutect_calls:
     input:
-        vcf="variant/{sample}.vcf",
-        ref="genome.fasta",
-        ref_dict="genome.dict",
-        ref_fai="genome.fasta.fai",
-        bam="picard/{sample}.bam",
-        bam_bai="picard/{sample}.bam.bai",
-        contamination="contamination/{sample}.pileups.table",
-        f1r2="artifacts_prior/{sample}.tar.gz",
+        vcf="<results>/variant/<per>.vcf",
+        ref="<genome_sequence>",
+        ref_dict="<genome_dict>",
+        ref_fai="<genome_sequence_index>",
+        bam="<results>/picard/<per>.bam",
+        bam_bai="<results>/picard/<per>.bam.bai",
+        contamination="<results>/contamination/<per>.pileups.table",
+        f1r2="<results>/artifacts_prior/<per>.tar.gz",
     output:
-        vcf="variant/{sample}.filtered.vcf.gz",
-        vcf_idx="variant/{sample}.filtered.vcf.gz.tbi",
+        vcf="<results>/variant/<per>.filtered.vcf.gz",
+        vcf_idx="<results>/variant/<per>.filtered.vcf.gz.tbi",
     threads: 1
     resources:
         mem_mb=1024,
     log:
-        "logs/gatk/filter/{sample}.log",
+        "<logs>/gatk/filter/<per>.log",
     params:
         extra="--create-output-variant-index --min-median-mapping-quality 35 --max-alt-allele-count 3",
         java_opts="",

meta/bio/gatk_mutect2_calling/test/Snakefile

@@ -2,7 +2,13 @@ from snakemake.utils import min_version
 
 min_version("9.13.1")
 
+
+configfile: "config.yaml"
+
+
 module gatk_mutect2_calling:
-    meta_wrapper: "master/meta/bio/gatk_mutect2_calling"
+    meta_wrapper:
+        "master/meta/bio/gatk_mutect2_calling"
+
 
-use rule * from gatk_mutect2_calling
+use rule * from gatk_mutect2_calling

meta/bio/gatk_mutect2_calling/test/config.yaml

@@ -0,0 +1,9 @@
+pathvars:
+  genome_sequence: "reference/genome.fasta"
+  genome_sequence_index: "reference/genome.fasta.fai"
+  genome_dict: "reference/genome.dict"
+  bed_intervals: "reference/regions.bed"
+  known_variants: "reference/known.vcf.gz"
+  known_variants_tbi: "reference/known.vcf.gz.tbi"
+  per: "{sample}"
+  bam_file: "mapped/{sample}.bam"

test_wrappers.py

@@ -6559,7 +6559,7 @@ def test_gatk_mutect2_calling_meta(run):
             "2",
             "--use-conda",
             "-F",
-            "variant/Sample1.filtered.vcf.gz.tbi",
+            "results/variant/Sample1.filtered.vcf.gz.tbi",
         ],
     )