fix resources and snp output

seqnado/config.py

@@ -360,6 +360,7 @@ def setup_configuration(assay, genome, template_data):
 bcftools:
     threads: 16
     options:
+    filter:
     
 """
 

seqnado/design.py

@@ -1359,6 +1359,8 @@ def snp_files(self) -> List[str]:
         if self.call_snps:
             return expand(
                 "seqnado_output/variant/{method}/{sample}.vcf.gz",
+                "seqnado_output/variant/{method}/{sample}.anno.vcf.gz",
+                "seqnado_output/variant/{method}/{sample}/{sample}_summary.pdf",
                 sample=self.sample_names,
                 method=self.snp_calling_method,
             )
@@ -1388,55 +1390,3 @@ def files(self) -> List[str]:
             files.append(self.snp_files)
 
         return files
-
-
-class SNPOutput(Output):
-    assay: Literal["SNP"]
-    call_snps: bool = False
-    sample_names: List[str]
-    make_ucsc_hub: bool = False
-    snp_calling_method: Optional[
-        Union[
-            Literal["bcftools", "deepvariant", False],
-            List[Literal["bcftools", "deepvariant"]],
-        ]
-    ] = None
-
-    @property
-    def design(self):
-        return ["seqnado_output/design.csv"]
-
-    @property
-    def snp_files(self) -> List[str]:
-        if self.call_snps:
-            return expand(
-                "seqnado_output/variant/{method}/{sample}.vcf.gz",
-                sample=self.sample_names,
-                method=self.snp_calling_method,
-            )
-        else:
-            return []
-
-    @computed_field
-    @property
-    def files(self) -> List[str]:
-        files = []
-        files.extend(
-            QCFiles(
-                assay=self.assay,
-                fastq_screen=self.fastq_screen,
-                library_complexity=self.library_complexity,
-            ).files
-        )
-
-        for file_list in (
-            self.snp_files,
-            self.design,
-        ):
-            if file_list:
-                files.extend(file_list)
-
-        if self.call_snps:
-            files.append(self.snp_files)
-
-        return files

seqnado/workflow/envs/profiles/profile_slurm_singularity/config.yaml

@@ -14,8 +14,8 @@ retries: 3
 
 default-resources: 
     slurm_partition: "short"
-    runtime: "1h"
-    mem: "3G"
+    runtime: "8h"
+    mem: "10G"
 
 # local-storage-prefix: $TMPDIR
 # default-storage-provider: fs

seqnado/workflow/rules/fastq_trim.smk

@@ -9,10 +9,10 @@ rule trimgalore_paired:
     output:
         trimmed1=temp("seqnado_output/trimmed/{sample}_1.fastq.gz"),
         trimmed2=temp("seqnado_output/trimmed/{sample}_2.fastq.gz"),
-    threads: 4
     resources:
-        mem="2GB",
-        runtime="4h",
+        runtime=lambda wildcards, attempt: f"{6 * 2 ** (attempt - 1)}h",
+        mem=lambda wildcards, attempt: f"{4 * 2 ** (attempt - 1)}GB",
+    threads: config["trim_galore"]["threads"]
     params:
         options=check_options(config["trim_galore"]["options"]),
         trim_dir="seqnado_output/trimmed",

seqnado/workflow/rules/variant.smk

@@ -18,64 +18,67 @@ if config["call_snps"]:
         shell:
             "bcftools mpileup --threads {threads} -Ou -f {params.fasta} {input.bam} | bcftools call --threads {threads} -mv -Oz -o {output.vcf} > {log} 2>&1"
 
-    rule index_snp:
+    rule bcftools_split_multiallelic:
         input:
             vcf=rules.bcftools_call_snp.output.vcf,
         output:
-            vcf="seqnado_output/variant/bcftools/{sample}_filtered.vcf.gz.tbi",
-        shell:
-            "tabix -f {input.vcf} > {output.vcf}"
+            vcf="seqnado_output/variant/bcftools/{sample}.split.vcf.gz",
+        resources:
+            mem=lambda wildcards, attempt: f"{10 * 2 ** (attempt -1)}GB",
+            runtime=lambda wildcards, attempt: f"{6 * 2 ** (attempt - 1)}h",
+        threads: config["bcftools"]["threads"]
+        shell:"""
+        bcftools norm --threads {threads} -Ou -m - {input.vcf} -Oz -o {output.vcf}
+        tabix -f {output.vcf} > {output.vcf}.tbi
+        """
 
-
-    rule bcftools_stats:
+
+    rule bcftools_filter_snp:
+        input:
+            vcf=rules.bcftools_split_multiallelic.output.vcf,
+        output:
+            vcf="seqnado_output/variant/bcftools/{sample}.filtered.vcf.gz",
+        params:
+            options=check_options(config["bcftools"]["filter"]),
+        resources:
+            mem=lambda wildcards, attempt: f"{10 * 2 ** (attempt -1)}GB",
+            runtime=lambda wildcards, attempt: f"{6 * 2 ** (attempt - 1)}h",
+        threads: config["bcftools"]["threads"]
+        shell: """
+        bcftools view --threads {threads} {params.options} -Oz -o {output.vcf} {input.vcf} 
+        tabix -f {output.vcf} > {output.vcf}.tbi
+        """
+
+    rule bcftools_annotate:
         input:
             vcf=rules.bcftools_call_snp.output.vcf,
+            idx=rules.index_snp.output.vcf,
         output:
-            stats="seqnado_output/variant/bcftools/{sample}_filtered.stats.txt",
+            vcf="seqnado_output/variant/bcftools/{sample}.anno.vcf.gz",
         params:
-            fasta=config["fasta"],
+            dbsnp=config["snp_database"],
+        threads: config["bcftools"]["threads"]
         shell:
-            "bcftools stats -F {params.fasta} -s - {input.vcf} > {output.stats}"
+            "bcftools annotate --threads {threads} -a {params.dbsnp} -c ID -Oz -o {output.vcf} {input.vcf}"
 
-    rule bcftools_stats_plot:
+    rule bcftools_stats:
         input:
-            stats=rules.bcftools_stats.output.stats,
+            vcf=rules.bcftools_annotate.output.vcf,
         output:
-            summary="seqnado_output/variant/bcftools/{sample}_summary.pdf",
+            stats="seqnado_output/variant/bcftools/{sample}.anno.stats.txt",
         params:
             fasta=config["fasta"],
-            out_dir="seqnado_output/variant/bcftools/",
+        threads: config["bcftools"]["threads"]
         shell:
-            "plot-vcfstats -p {params.out_dir} {input.stats}"
+            "bcftools stats -F {params.fasta} -s - {input.vcf} > {output.stats}"
 
-    rule bcftools_annotate:
+    rule bcftools_stats_plot:
         input:
-            vcf=rules.bcftools_call_snp.output.vcf,
-            idx=rules.index_snp.output.vcf,
+            stats=rules.bcftools_stats.output.stats,
         output:
-            vcf="seqnado_output/variant/bcftools/{sample}_filtered.anno.vcf.gz",
+            summary="seqnado_output/variant/bcftools/{sample}/{sample}_summary.pdf",
         params:
-            dbsnp=config["snp_database"],
-        threads: 16
+            fasta=config["fasta"],
+            out_dir="seqnado_output/variant/bcftools/{sample}",
         shell:
-            "bcftools annotate --threads 16 -c ID -a {params.dbsnp} {input.vcf} > {output.vcf}"
-
-    # rule bcftools_split_multiallelic:
-    #     input:
-    #         vcf=rules.bcftools_call_snp.output.vcf,
-    #     output:
-    #         vcf="seqnado_output/variant/bcftools/{sample}_splitmultiallelic.vcf.gz",
-    #     shell:
-    #         "bcftools norm -m -any {input.vcf} -o {output.vcf} -Oz"
-
-    # rule bcftools_filter_snp:
-    #     input:
-    #         vcf=rules.bcftools_split_multiallelic.output.vcf,
-    #     output:
-    #         vcf="seqnado_output/variant/bcftools/{sample}_filtered.vcf.gz",
-    #     params:
-    #         options=check_options(config["bcftools"]["options"]),
-    #     shell:
-    #         """bcftools view {params.options} -o {output.vcf} {input.vcf}"""
-
-
+            "plot-vcfstats -p {params.out_dir} {input.stats}"