checkout preprocssing files from main

pipelines/preprocess_no_qc.snakefile

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+include: "preprocessing/preprocess.snakefile"
+
+
+rule all:
+    input:
+        preprocessed_dir / "genotypes.h5",
+        norm_variants_dir / "variants.tsv.gz",
+        variants=norm_variants_dir / "variants.parquet",
+
+
+rule preprocess_no_qc:
+    input:
+        variants=norm_variants_dir / "variants.tsv.gz",
+        variants_parquet=norm_variants_dir / "variants.parquet",
+        samples=norm_dir / "samples_chr.csv",
+        sparse_tg=expand(sparse_dir / "{vcf_stem}.tsv.gz", vcf_stem=vcf_stems),
+    output:
+        expand(preprocessed_dir / "genotypes_chr{chr}.h5", chr=chromosomes),
+    shell:
+        " ".join(
+            [
+                f"{preprocessing_cmd}",
+                "process-sparse-gt",
+                f"--exclude-variants {qc_duplicate_vars_dir}",
+                "--chromosomes ",
+                ",".join(str(chr) for chr in set(chromosomes)),
+                f"--threads {preprocess_threads}",
+                "{input.variants}",
+                "{input.samples}",
+                f"{sparse_dir}",
+                f"{preprocessed_dir / 'genotypes'}",
+            ]
+        )

pipelines/preprocess_with_qc.snakefile

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+
+include: "preprocessing/preprocess.snakefile"
+include: "preprocessing/qc.snakefile"
+
+
+rule all:
+    input:
+        preprocessed_dir / "genotypes.h5",
+        norm_variants_dir / "variants.tsv.gz",
+        variants=norm_variants_dir / "variants.parquet",
+
+
+rule preprocess_with_qc:
+    input:
+        variants=norm_variants_dir / "variants.tsv.gz",
+        variants_parquet=norm_variants_dir / "variants.parquet",
+        samples=norm_dir / "samples_chr.csv",
+        sparse_tg=expand(sparse_dir / "{vcf_stem}.tsv.gz", vcf_stem=vcf_stems),
+        qc_varmiss=expand(qc_varmiss_dir / "{vcf_stem}.tsv.gz", vcf_stem=vcf_stems),
+        qc_hwe=expand(qc_hwe_dir / "{vcf_stem}.tsv.gz", vcf_stem=vcf_stems),
+        qc_read_depth=expand(
+            qc_read_depth_dir / "{vcf_stem}.tsv.gz", vcf_stem=vcf_stems
+        ),
+        qc_allelic_imbalance=expand(
+            qc_allelic_imbalance_dir / "{vcf_stem}.tsv.gz", vcf_stem=vcf_stems
+        ),
+        qc_filtered_samples=qc_filtered_samples_dir,
+    output:
+        expand(preprocessed_dir / "genotypes_chr{chr}.h5", chr=chromosomes),
+    shell:
+        " ".join(
+            [
+                f"{preprocessing_cmd}",
+                "process-sparse-gt",
+                f"--exclude-variants {qc_allelic_imbalance_dir}",
+                f"--exclude-variants {qc_hwe_dir}",
+                f"--exclude-variants {qc_varmiss_dir}",
+                f"--exclude-variants {qc_duplicate_vars_dir}",
+                f"--exclude-calls {qc_read_depth_dir}",
+                f"--exclude-samples {qc_filtered_samples_dir}",
+                "--chromosomes ",
+                ",".join(str(chr) for chr in set(chromosomes)),
+                f"--threads {preprocess_threads}",
+                "{input.variants}",
+                "{input.samples}",
+                f"{sparse_dir}",
+                f"{preprocessed_dir / 'genotypes'}",
+            ]
+        )