Add smash rule

src/snakemake/rules/bedtools_intersect.smk

@@ -1,4 +1,4 @@
-"""
+ """
 Note:
     Depending on your needs, you may rather use on of these three rules:
     bedtools_intersect_b_lambda_extra

src/snakemake/rules/smash.smk

@@ -0,0 +1,51 @@
+rule smash_dir:
+    """
+    Aim:
+        First used to select subpopulations from bam.
+        Trying this:
+        https://www.biostars.org/p/225198/
+    Note:
+    Test:
+        out/smash/vcf-SMaSH-snps-GRCh38/ln/alias/sst/by_run/run356/GRCh38/bam/pval_out.txt
+
+    """
+    input:
+        # bam_list = lambda wildcards: config["bam_list"][wildcards.filler],
+        # BAMs must end in .bam and be indexed
+        vcf = lambda wildcards: eval(mwconf['ids'][wildcards.vcf_id]),
+        py = "out/wget/https/raw.githubusercontent.com/rbundschuh/SMaSH/master/SMaSH.py"
+    output:
+        # TODO: Look for multiqc_dir rule to do the same
+        tsv = "out/{tool}{extra}{vcf_id}/{filler}/pval_out.txt"
+    params:
+        indir = "out/{filler}",
+        outdir = "out/{tool}{extra}{vcf_id}/{filler}"
+    log:
+        "out/{tool}{extra}{vcf_id}/{filler}.log"
+    benchmark:
+        "out/{tool}{extra}{vcf_id}/{filler}.benchmark.tsv"
+    params:
+        extra = params_extra
+    threads:
+        MAX_THREADS
+    wildcard_constraints:
+        tool = "smash/"
+    conda:
+        "../envs/smash.yaml"
+    shell:
+        """
+        (
+        mkdir -p {params.outdir}
+
+        for ext in bam bam.bai
+        do
+            for file in "{params.indir}/"*.$ext
+            do
+                ln -srf "$file" "{params.outdir}"
+            done
+        done
+        cd {params.outdir}
+
+        python {WDIR}/{input.py} -i {WDIR}/{input.vcf} -bam ALL
+        ) &> {log}
+        """