if config["bam2bakr"]:
    if config["remove_tags"]:

        rule remove_tags:
            input:
                input_bam=get_input_bams,
            output:
                output_bam="results/remove_tags/{sample}_no_jI_jM.bam",
            log:
                "logs/remove_tags/{sample}.log",
            conda:
                "../envs/full.yaml"
            script:
                "../scripts/remove_tags.py"

        # Filter out multi-mappers and sort reads
        rule sort_filter:
            input:
                "results/remove_tags/{sample}_no_jI_jM.bam",
            output:
                "results/sf_reads/{sample}.s.bam",
                "results/sf_reads/{sample}_fixed_mate.bam",
                "results/sf_reads/{sample}.f.sam",
            log:
                "logs/sort_filter/{sample}.log",
            params:
                shellscript=workflow.source_path("../scripts/sort_filter.sh"),
            threads: 8
            conda:
                "../envs/full.yaml"
            shell:
                """
                chmod +x {params.shellscript}
                {params.shellscript} {threads} {wildcards.sample} {input} {output} {config[FORMAT]} 1> {log} 2>&1
                """

    else:

        # Filter out multi-mappers and sort reads
        rule sort_filter:
            input:
                get_input_bams,
            output:
                "results/sf_reads/{sample}.s.bam",
                "results/sf_reads/{sample}_fixed_mate.bam",
                "results/sf_reads/{sample}.f.sam",
            log:
                "logs/sort_filter/{sample}.log",
            params:
                shellscript=workflow.source_path("../scripts/sort_filter.sh"),
            threads: 8
            conda:
                "../envs/full.yaml"
            shell:
                """
                chmod +x {params.shellscript}
                {params.shellscript} {threads} {wildcards.sample} {input} {output} {config[FORMAT]} 1> {log} 2>&1
                """

else:

    # Filter out multi-mappers and sort reads
    rule sort_filter:
        input:
            "results/bams/{sample}Aligned.out.bam",
        output:
            "results/sf_reads/{sample}.s.bam",
            "results/sf_reads/{sample}_fixed_mate.bam",
            "results/sf_reads/{sample}.f.sam",
        log:
            "logs/sort_filter/{sample}.log",
        params:
            shellscript=workflow.source_path("../scripts/sort_filter.sh"),
            read_format=config["FORMAT"],
        threads: 8
        conda:
            "../envs/full.yaml"
        shell:
            """
            chmod +x {params.shellscript}
            {params.shellscript} {threads} {wildcards.sample} {input} {output} {params.read_format} 1> {log} 2>&1
            """


# Calculate normalization scale factor to be applied to tracks
if NORMALIZE:

    rule normalize:
        input:
            expand(
                "results/featurecounts_exons/{sample}.featureCounts", sample=SAMP_NAMES
            ),
        output:
            "results/normalization/scale",
        log:
            "logs/normalize/normalize.log",
        threads: 1
        params:
            rscript=workflow.source_path("../scripts/normalize.R"),
            spikename=config["spikename"],
        conda:
            "../envs/full.yaml"
        shell:
            r"""
            chmod +x {params.rscript}
            {params.rscript} --dirs ./results/featurecounts_exons/ --output {output} --spikename {params.spikename} 1> {log} 2>&1
            """

else:

    rule normalize:
        input:
            expand("results/sf_reads/{sample}.s.bam", sample=SAMP_NAMES),
        output:
            "results/normalization/scale",
        log:
            "logs/normalize/normalize.log",
        threads: 1
        conda:
            "../envs/full.yaml"
        shell:
            """
            touch {output}
            """


# Index genome fasta file for snp calling
rule index:
    input:
        str(config["genome_fasta"]),
    output:
        get_index_name(),
    log:
        "logs/genome-faidx.log",
    threads: 1
    conda:
        "../envs/index.yaml"
    script:
        "../scripts/genome-faidx.py"


# Identify SNPs to be accounted for when counting mutations
rule call_snps:
    input:
        str(config["genome_fasta"]),
        get_index_name(),
        expand("results/sf_reads/{ctl}.s.bam", ctl=CTL_NAMES),
    params:
        nctl=nctl,
        shellscript=workflow.source_path("../scripts/call_snps.sh"),
    output:
        "results/snps/snp.txt",
        "results/snps/snp.vcf",
        temp("results/snps/mkdir.txt"),
    log:
        "logs/call_snps/ctl_samps.log",
    threads: 20
    conda:
        "../envs/full.yaml"
    shell:
        """
        chmod +x {params.shellscript}
        {params.shellscript} {threads} {params.nctl} {output} {input} 1> {log} 2>&1
        """


# TO-DO:
# 1) Add mutation position optimizations and functionality
# Count mutations
rule cnt_muts:
    input:
        "results/sf_reads/{sample}.s.bam",
        "results/snps/snp.txt",
    params:
        format=FORMAT,
        minqual=config["minqual"],
        mut_tracks=config["mut_tracks"],
        strand=config["strandedness"],
        shellscript=workflow.source_path("../scripts/mut_call.sh"),
        pythonscript=workflow.source_path("../scripts/mut_call.py"),
        awkscript=workflow.source_path("../scripts/fragment_sam.awk"),
        mutpos=False,
    output:
        "results/counts/{sample}_counts.csv.gz",
        temp("results/counts/{sample}_check.txt"),
    log:
        "logs/cnt_muts/{sample}.log",
    threads: 32
    conda:
        "../envs/full.yaml"
    shell:
        """
        chmod +x {params.shellscript}
        chmod +x {params.pythonscript}
        chmod +x {params.awkscript}
        {params.shellscript} {threads} {wildcards.sample} {input} {output} {params.minqual} {params.mut_tracks} {params.format} {params.strand} {params.pythonscript} {params.awkscript} {params.mutpos} 1> {log} 2>&1
        """


# Merge mutation counts with feature assignment
rule merge_features_and_muts:
    input:
        get_merge_input,
    output:
        "results/merge_features_and_muts/{sample}_counts.csv.gz",
    params:
        genes_included=config["features"]["genes"],
        exons_included=config["features"]["exons"],
        exonbins_included=False,
        transcripts_included=False,
        rscript=workflow.source_path("../scripts/merge_features_and_muts.R"),
    log:
        "logs/merge_features_and_muts/{sample}.log",
    threads: 20
    conda:
        "../envs/rstuff.yaml"
    shell:
        """
        chmod +x {params.rscript}

        {params.rscript} -g {params.genes_included} -e {params.exons_included} -b {params.exonbins_included} \
        -t {params.transcripts_included} -o {output} -s {wildcards.sample} 1> {log} 2>&1
        """


# Make color-coded tracks
rule maketdf:
    input:
        "results/counts/{sample}_counts.csv.gz",
        "results/sf_reads/{sample}.s.bam",
        "results/normalization/scale",
    output:
        temp("results/tracks/{sample}_success.txt"),
        expand(
            "results/tracks/{{sample}}.{mut}.{id}.{strand}.tdf",
            mut=Mutation_Types,
            id=[0, 1, 2, 3, 4, 5],
            strand=["pos", "min"],
        ),
    params:
        shellscript=workflow.source_path("../scripts/tracks.sh"),
        pythonscript=workflow.source_path("../scripts/count_to_tracks.py"),
        mut_tracks=config["mut_tracks"],
        genome_fasta=config["genome_fasta"],
        wsl=config["WSL"],
        normalize=config["normalize"],
    log:
        "logs/maketdf/{sample}.log",
    threads: 20
    conda:
        "../envs/full.yaml"
    shell:
        """
        chmod +x {params.shellscript}
        chmod +x {params.pythonscript}
        {params.shellscript} {threads} {wildcards.sample} {input} {params.mut_tracks} {params.genome_fasta} {params.wsl} {params.normalize} {params.pythonscript} {output} 1> {log} 2>&1
        """


# Make cB file that will be input to bakR
rule makecB:
    input:
        expand(
            "results/merge_features_and_muts/{sample}_counts.csv.gz",
            sample=config["samples"],
        ),
    output:
        cB="results/cB/cB.csv.gz",
    params:
        shellscript=workflow.source_path("../scripts/master.sh"),
        keepcols=keepcols,
        mut_tracks=config["mut_tracks"],
        mut_pos=False,
    log:
        "logs/makecB/master.log",
    threads: 20
    conda:
        "../envs/full.yaml"
    shell:
        """
        chmod +x {params.shellscript}
        {params.shellscript} {threads} {output.cB} {params.keepcols} {params.mut_tracks} \
        ./results/merge_features_and_muts/ {params.mut_pos} 1> {log} 2>&1
        """