shell:
    "(multiqc -f {input} -o aggregated/QC_pe/) 2> {log}"

shell:
    "(multiqc -f {input} -o aggregated_spikein/QC_pe/) 2> {log}"

shell:
    "(multiqc -f {input} -o aggregated/QC_se/) 2> {log}"

shell:
    "head -n 1 {input[0]} > {output} && "
    "cat {input} | sed '1~2d' >> {output}"

shell:
    "head -n 1 {input[0]} > {output} && "
    "cat {input} | sed '1~2d' >> {output}"

shell:
    "(Rscript --vanilla {params.scr_dir}/workflow/scripts/aggr_qc_report.R "
    "{params.aggr} {params.ispaired} {input} {params.scr_dir} {params.out_dir}) 2> {log}"

shell:
    "(cp {input.bin1} {output.bin1} && paste {output.bin1} {input.mb1}  >  {output.mb1} && "
    " cp {input.bin5} {output.bin5} && paste {output.bin5} {input.mb5}  >  {output.mb5}) 2> {log}"

shell:
    "(cp {input.bin}  {output.bin} && "
    "paste {output.bin} {input.cnt}  | bgzip > {output.cnt} && tabix -p bed {output.cnt} && "
    "paste {output.bin} {input.rpkm} | bgzip > {output.rpkm} && tabix -p bed {output.rpkm})  2> {log}"

shell:
    "tabix -p bed -R {input.bin} -h {input.cnt} | bgzip > {output.cnt} && tabix -p bed {output.cnt} && "
    "tabix -p bed -R {input.bin} -h {input.rpkm} | bgzip > {output.rpkm} && tabix -p bed {output.rpkm} && "
    "tabix -p bed -R {input.bin} -h {input.CNV_qsea}   |  bgzip > {output.CNV_qsea} && tabix -p bed {output.CNV_qsea} && "
    "tabix -p bed -R {input.bin} -h {input.beta_qsea}  |  bgzip > {output.beta_qsea} && tabix -p bed {output.beta_qsea} && "
    "tabix -p bed -R {input.bin} -h {input.nrpm_qsea}  |  bgzip > {output.nrpm_qsea} && tabix -p bed {output.nrpm_qsea} && "
    "tabix -p bed -R {input.bin} -h {input.rms_medips} |  bgzip > {output.rms_medips} && tabix -p bed {output.rms_medips} && "
    "tabix -p bed -R {input.bin} -h {input.rms_medestrand} | bgzip > {output.rms_medestrand} && tabix -p bed {output.rms_medestrand} && "
    "tabix -p bed -R {input.bin} -h {input.logitbeta_qsea} | bgzip > {output.logitbeta_qsea} && tabix -p bed {output.logitbeta_qsea}"

shell:
    'touch {output}'

shell:
    'touch {output}'

shell:
    'touch {output}'

shell:
    'touch {output}'

shell:
    'touch {output}'

shell:
    'touch {output}'

shell:
    'touch {output}'

shell:
    "(Rscript --vanilla {params.scr_dir}/workflow/scripts/fragment_profile.R "
    "{wildcards.sample} {input} {params.bsgenome} {params.scr_dir}) 2> {log}"

shell:
    "(samtools view -b -f 2 -F 2828 --threads {threads} {input} | "
    "samtools markdup -@ {threads} -r - {output.bam} && "
    "samtools index -@ {threads} {output.bam} && "
    "samtools stats -@ {threads} {output.bam} > {output.stat})"

shell:
    "(samtools view -b -F 2820 --threads {threads} {input} | "
    "samtools markdup -@ {threads} -r - {output.bam} && "
    "samtools index -@ {threads} {output.bam} && "
    "samtools stats -@ {threads} {output.bam} > {output.stat})"

shell:
    "(java -jar {params.pipeline_env}/share/picard-2.26.6-0/picard.jar "
    "CollectInsertSizeMetrics M=0.05 I={input} O={output.txt} "
    "H={output.hist}) 2> {log}"

shell:
    "(Rscript --vanilla {params.scr_dir}/workflow/scripts/medips_medestrand_qsea.R "
    "{wildcards.sample} {input} {params.bsgenome} {params.ispaired} {params.window_size} "
    "{params.scr_dir}/workflow/dependencies/MeDEStrand) 2> {log}"

shell:
    "(Rscript --vanilla {params.scr_dir}/workflow/scripts/medips_4spikein.R "
    "{wildcards.sample} {input} {params.ispaired} {params.window_size} "
    "{params.bsgenome} {params.scr_dir}/assets/Spike-in_genomes/{params.bsgenome_pkg}) 2> {log}"

shell:
    "cat {input} > {output}"

    shell:
        "cat {input.R1} > {output[0]} && "
        "cat {input.R2} > {output[1]} "

"""
## Obsoleted !!
###########################################################
### extract UMI barcode and add it to FASTQ headers, p.r.n.
### pair-end unzipped FASTQ only with ConsensusCruncher
###########################################################
rule extract_barcode:
    input:
        get_renamed_fastq
    output:
        temp("barcoded_fq/{sample}_R1.fastq"),
        temp("barcoded_fq/{sample}_R2.fastq"),
        "barcoded_fq/{sample}_R1.fastq.gz",
        "barcoded_fq/{sample}_R2.fastq.gz"
    conda:
        "extra_env/ConsensusCruncher.yaml"
    params:
        src = pipe_dir + "/workflow/dependencies/ConsensusCruncher/ConsensusCruncher/extract_barcodes.py",
        blist = umi_list,                 ## barcode list
        outfile = "barcoded_fq/{sample}"
    shell:
        ## unzip gz files
        "gunzip {input[0]} -c > {params.outfile}_R1.fastq && "
        "gunzip {input[1]} -c > {params.outfile}_R2.fastq && "

        ## extract barcodes
        #"python  {params.src} --bpattern NNT "
        "python  {params.src} --blist {params.blist} "
        "--read1  {input[0]}  --read2   {input[1]} "
        "--outfile  {params.outfile} && "

        ## gzip
        "gzip  {params.outfile}_barcode_R*.fastq  && "

        ## change to consistant names for following steps
        "mv {params.outfile}_barcode_R1.fastq.gz  {params.outfile}_R1.fastq.gz && "
        "mv {params.outfile}_barcode_R2.fastq.gz  {params.outfile}_R2.fastq.gz"
"""

shell:
    "umi_tools extract --extract-method=regex "
    "--stdin={input[0]} --bc-pattern={params.bcp} "
    "--stdout={output[0]}  --log={output[1]}"

shell:
    "(trim_galore -q 20 --stringency 3 --length 20 "
    "--cores {threads} -o {params.path} {input}) 2> {log}"

shell:
    "(trim_galore -q 20 --stringency 3 --length 20 "
    "--cores {threads} --paired -o {params.path} {input}) 2> {log}"

run:
    for fq in input:
        shell("fastqc {} -t 8 --outdir fastqc_pe/".format(fq))