refactors expand

workflow/Snakefile

@@ -53,20 +53,20 @@ rule all:
         OUT_DIR / "project_level_qc" / "somalier" / "ancestry" / "somalier.somalier-ancestry.html",
         ##### coverage #####
         # samtools
-        expand(str(OUT_DIR / "{sample}" / "qc" / "samtools-stats" / "{sample}.txt"), sample=SAMPLES),
+        expand(OUT_DIR / "{sample}" / "qc" / "samtools-stats" / "{sample}.txt", sample=SAMPLES),
         # qualimap
-        expand(str(OUT_DIR / "{sample}" / "qc" / "qualimap" / "{sample}" / "qualimapReport.html"), sample=SAMPLES),
+        expand(OUT_DIR / "{sample}" / "qc" / "qualimap" / "{sample}" / "qualimapReport.html", sample=SAMPLES),
         # mosdepth
-        expand(str(OUT_DIR / "{sample}" / "qc" / "mosdepth" / "{sample}.mosdepth.global.dist.txt"), sample=SAMPLES),
+        expand(OUT_DIR / "{sample}" / "qc" / "mosdepth" / "{sample}.mosdepth.global.dist.txt", sample=SAMPLES),
         OUT_DIR / "project_level_qc" / "mosdepth" / "mosdepth.html",
         # indexcov and covviz
         WGS_ONLY_COVERAGE_TARGETS,
         ##### cross-sample contamination #####
         # verifyBamID
-        expand(str(OUT_DIR / "{sample}" / "qc" / "verifyBamID" / "{sample}.Ancestry"), sample=SAMPLES),
+        expand(OUT_DIR / "{sample}" / "qc" / "verifyBamID" / "{sample}.Ancestry", sample=SAMPLES),
         ##### VCF stats #####
         # bcftools
-        expand(str(OUT_DIR / "{sample}" / "qc" / "bcftools-stats" / "{sample}.bcftools.stats"), sample=SAMPLES),
+        expand(OUT_DIR / "{sample}" / "qc" / "bcftools-stats" / "{sample}.bcftools.stats", sample=SAMPLES),
         ##### results aggregation #####
-        expand(str(OUT_DIR / "{sample}" / "qc" / "multiqc_final_pass" / "{sample}_multiqc.html"), sample=SAMPLES),
+        expand(OUT_DIR / "{sample}" / "qc" / "multiqc_final_pass" / "{sample}_multiqc.html", sample=SAMPLES),
         OUT_DIR / "project_level_qc" / "multiqc" / "multiqc_report.html",

workflow/rules/aggregate_results.smk

@@ -133,8 +133,8 @@ rule multiqc_aggregation_all_samples:
         # using custom rename config file
         extra=(
             lambda wildcards, input: f'--config {input.multiqc_config} \
-                    --sample-names {input.rename_config} \
-                    --cl_config "max_table_rows: 2000"'
+                            --sample-names {input.rename_config} \
+                            --cl_config "max_table_rows: 2000"'
         ),
     wrapper:
         "0.64.0/bio/multiqc"

workflow/rules/coverage_analysis.smk

@@ -71,7 +71,7 @@ rule mosdepth_coverage:
 
 rule mosdepth_plot:
     input:
-        dist=expand(str(OUT_DIR / "{sample}" / "qc" / "mosdepth" / "{sample}.mosdepth.global.dist.txt"), sample=SAMPLES),
+        dist=expand(OUT_DIR / "{sample}" / "qc" / "mosdepth" / "{sample}.mosdepth.global.dist.txt", sample=SAMPLES),
         script=WORKFLOW_PATH / "src/mosdepth/v0.3.1/plot-dist.py",
     output:
         OUT_DIR / "project_level_qc" / "mosdepth" / "mosdepth.html",
@@ -94,11 +94,11 @@ rule mosdepth_plot:
 rule indexcov:
     input:
         bam=expand(
-            str(PROJECT_PATH / "{sample}" / "bam" / "{sample}.bam"),
+            PROJECT_PATH / "{sample}" / "bam" / "{sample}.bam",
             sample=SAMPLES,
         ),
         bam_index=expand(
-            str(PROJECT_PATH / "{sample}" / "bam" / "{sample}.bam.bai"),
+            PROJECT_PATH / "{sample}" / "bam" / "{sample}.bam.bai",
             sample=SAMPLES,
         ),
     output:

workflow/rules/relatedness_ancestry.smk

@@ -26,11 +26,11 @@ rule somalier_extract:
 
 rule somalier_relate:
     input:
-        extracted=expand(str(OUT_DIR / "project_level_qc" / "somalier" / "extract" / "{sample}.somalier"), sample=SAMPLES),
+        extracted=expand(OUT_DIR / "project_level_qc" / "somalier" / "extract" / "{sample}.somalier", sample=SAMPLES),
         ped=PEDIGREE_FPATH,
     output:
         out=expand(
-            str(OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.{ext}"),
+            OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.{ext}",
             ext=["html", "pairs.tsv", "samples.tsv"],
         ),
     message:
@@ -57,12 +57,12 @@ rule somalier_relate:
 
 rule somalier_ancestry:
     input:
-        extracted=expand(str(OUT_DIR / "project_level_qc" / "somalier" / "extract" / "{sample}.somalier"), sample=SAMPLES),
+        extracted=expand(OUT_DIR / "project_level_qc" / "somalier" / "extract" / "{sample}.somalier", sample=SAMPLES),
         labels_1kg=config["somalier"]["labels_1kg"],
         somalier_1kg=directory(config["somalier"]["somalier_1kg"]),
     output:
         out=expand(
-            str(OUT_DIR / "project_level_qc" / "somalier" / "ancestry" / "somalier.somalier-ancestry.{ext}"),
+            OUT_DIR / "project_level_qc" / "somalier" / "ancestry" / "somalier.somalier-ancestry.{ext}",
             ext=["html", "tsv"],
         ),
     message: