Initial pipeline that does part of the job

Snake.config.json

+{
+    "sample"        : "D2Rfb",
+
+
+    "mosaicatcher"  : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/build/mosaicatcher",
+    "plot_script"   : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/R/qc.R",
+    "sce_script"    : "/g/korbel/meiers/tools/mosaicatcher/strandsequtils/sce_utils/SCE.R",
+    "samtools"      : "module load SAMtools && samtools",
+
+
+    "exclude_file"  : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/data/exclude/hg19.exclude",
+    "variable_bins" : {
+        "50000"     : "utils/variable_bins.GRCh38.50kb.bed",
+        "100000"    : "utils/variable_bins.GRCh38.100kb.bed"
+    }
+}

Snakefile

+configfile: "Snake.config.json"
+
+BAM, = glob_wildcards("bam/{bam}.bam")
+
+# Current state of the pipeline:
+# ==============================
+# * count reads in the BAM files (in fixed and variable-width bins of various sizes)
+# * determine strand states of each chromosome in each single cell, including SCEs
+# * plot all single cell libraries in different window sizes
+# * calculate a segmentation into potential SVs using Mosaicatcher
+
+rule all:
+    input:
+        expand("plots/" + config["sample"] + "_{window}_fixed.pdf", window = [50000, 100000, 200000, 500000]),
+        expand("plots/" + config["sample"] + "_{window}_variable.pdf", window = [50000, 100000]),
+        expand("segmentation/" + config["sample"] + "_{window}_fixed.txt", window = [50000, 100000, 200000, 500000]),
+        expand("segmentation/" + config["sample"] + "_{window}_variable.txt", window = [50000, 100000]),
+        "strand_states/" + config["sample"] + ".txt"
+
+rule plot_mosaic_counts:
+    input:
+        counts = "counts/" + config["sample"] + "_{file_name}.txt.gz",
+        info   = "counts/" + config["sample"] + "_{file_name}.info"
+    output:
+        "plots/" + config["sample"] + "_{file_name}.pdf"
+    params: 
+        plot_command = "Rscript " + config["plot_script"]
+    shell:
+        """
+        {params.plot_command} {input.counts} {input.info} {output}
+        """
+
+rule mosaic_count_fixed:
+    input:
+        bam = expand("bam/" + config["sample"] + "_{bam}.bam", bam = BAM),
+        bai = expand("bam/" + config["sample"] + "_{bam}.bam.bai", bam = BAM)
+    output:
+        counts = "counts/" + config["sample"] + "_{window}_fixed.txt.gz",
+        info   = "counts/" + config["sample"] + "_{window}_fixed.info"
+    params:
+        mc_command = config["mosaicatcher"],
+        mc_exclfile = config["exclude_file"]
+    shell:
+        """
+        {params.mc_command} count \
+            -o {output.counts} \
+            -i {output.info} \
+            -x {params.mc_exclfile} \
+            -w {wildcards.window} \
+            {input.bam}
+        """
+
+
+rule mosaic_count_variable:
+    input:
+        bam = expand("bam/{bam}.bam", bam = BAM),
+        bai = expand("bam/{bam}.bam.bai", bam = BAM),
+        bed = lambda wc: config["variable_bins"][str(wc.window)]
+    output:
+        counts = "counts/" + config["sample"] + "_{window}_variable.txt.gz",
+        info   = "counts/" + config["sample"] + "_{window}_variable.info"
+    params:
+        mc_command = config["mosaicatcher"]
+    shell:
+        """
+        {params.mc_command} count \
+            -o {output.counts} \
+            -i {output.info} \
+            -b {input.bed} \
+            {input.bam}
+        """
+
+
+
+
+rule determine_strand_states:
+    input:
+        "counts/" + config["sample"] + "_500000_fixed.txt.gz"
+    output:
+        "strand_states/" + config["sample"] + ".txt"
+    params:
+        sce_command = "Rscript " + config["sce_script"]
+    shell:
+        """
+        {params.sce_command} {input} {output}
+        """
+
+
+rule segmentation:
+    input:
+        "counts/" + config["sample"] + "_{file_name}.txt.gz"
+    output:
+        "segmentation/" + config["sample"] + "_{file_name}.txt"
+    params:
+        mc_command = config["mosaicatcher"]
+    shell:
+        """
+        {params.mc_command} segment \
+        -o {output} \
+        {input}
+        """
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