shell:
    """
    pigz -p {threads} -c {input.valid_pairs} > {output.valid_pairs}
    """

shell:
    """
    pigz -p {threads} -c {input.matrix} > {output.matrix}
    """

shell:
    """
    ## The generic copy all. Clearly this will repeat every time though
    # cp {params.in_path}/* {params.out_path}

    ## Copy the specific files
    cp {input.stat} {output.stat}
    """

shell:
    """
    convert \
        -density {params.density} \
        {input.pdf}[0] \
        -quality {params.quality} \
        {output.png}
    """

shell:
    """
    Rscript --vanilla \
      {input.script} \
      {params.bin} &> {log}
    """

shell:
    """
    # Run the python script
    python {params.script} \
      -r {params.restriction_site} \
      -o {output.rs} \
      {input}
    """

shell:
    """
    awk '{{print($3 - $2)}}' {input} | \
      sort -n | \
      uniq -c > {output}
    """

shell:
    """
    pigz -p {threads} -c {input} > {output}
    """

shell:
    """
    Rscript --vanilla \
      scripts/write_hicpro_config.R \
      {params.idx_root} \
      {input.chr_sizes} \
      {input.rs} \
      {params.template} \
      {output}
    """

shell:
    """
    HiC-Pro \
      -s quality_checks \
      -c {input.config} \
      -i {params.indir} \
      -o {params.outdir} 
    """

shell:
    """
    HiC-Pro \
      -s proc_hic \
      -c {input.config} \
      -i {params.indir} \
      -o {params.outdir} 
    """

shell:
    """
    HiC-Pro \
      -s merge_persample \
      -c {input.config} \
      -i {params.indir} \
      -o {params.outdir} 
    """

shell:
    """
    HiC-Pro \
      -s build_contact_maps \
      -c {input.config} \
      -i {params.indir} \
      -o {params.outdir} 
    """

shell:
    """
    git clone https://github.com/Rassa-Gvm/MaxHiC.git scripts/MaxHiC
    rm -rf scripts/MaxHiC/Sample_Inputs
    """

shell:
    """
    ## Given the problems with the raw output from HiC-Pro, we should
    ## delete any *ord.bed* files that exist. They seem to have been 
    ## excluded from HiC-Pro v3
    if compgen -G "{params.input_path}/*ord.bed" > /dev/null; then
      echo -e "Deleting unnecessary symlink"
      rm {params.input_path}/*ord.bed
    fi

    python {input.maxhic_exe} \
      -t {threads} \
      {params.input_path} \
      {params.output_path} &> {log}

    ## Compress the output files
    pigz -p {threads} {params.output_path}/*txt
    """

shell:
    """
    Rscript --vanilla \
        scripts/merge_matrices.R \
        {params.bin} \
        {params.in_path} \
        {params.out_path} \
        {params.samples} &> {log}
    """

shell:
    """
    pigz -p {threads} -c {input.mat} > {output.mat}
    pigz -p {threads} -c {input.bed} > {output.bed}
    """

shell:
    """
    # Write to a separate temp directory for each run to avoid I/O clashes
    TEMPDIR=$(mktemp -d -t fqcXXXXXXXXXX)
    fastqc \
      {params} \
      -t {threads} \
      --outdir $TEMPDIR \
      {input} &> {log}

    # Move the files
    mv $TEMPDIR/*html $(dirname {output.html})
    mv $TEMPDIR/*zip $(dirname {output.zip})

    # Clean up the temp directory
    rm -rf $TEMPDIR
    """

shell:
    """
    wget \
      -O "{output}" \
      -o {log} \
      {params.ftp}
    """

shell:
    """
    gunzip -c {input} > {output}
    """

    shell:
        """
        # Download the assembly report
        TEMPDIR=$(mktemp -d -t chrXXXXXXXXXX)
        REPORT="assembly_report.txt"
	    curl {params.ftp} > $TEMPDIR/$REPORT 2> {log}

        # Extract the chrom_sizes
        egrep 'assembled-molecule' "$TEMPDIR/$REPORT" | \
          awk '{{print "chr"$2"\t"$3}}' > {output}

        rm -rf $TEMPDIR
        """

shell:
    """
    echo -e "Version: 1.0\n\nRestoreWorkspace: Default\nSaveWorkspace: Default\nAlwaysSaveHistory: Default\n\nEnableCodeIndexing: Yes\nUseSpacesForTab: Yes\nNumSpacesForTab: 2\nEncoding: UTF-8\n\nRnwWeave: knitr\nLaTeX: pdfLaTeX\n\nAutoAppendNewline: Yes\nStripTrailingWhitespace: Yes" > {output}
    """

shell:
    """
    git add analysis/*
    R -e "workflowr::wflow_build('{input.rmd}')" 2>&1 > {log}
    git add docs/*
    git commit -m 'Updated all'
    """

shell:
    """
    R -e "workflowr::wflow_build('{input.rmd}')" 2>&1 > {log}
    """

shell:
    """
    R -e "workflowr::wflow_build('{input.rmd}')" 2>&1 > {log}
    """

shell:
    """
    R -e "workflowr::wflow_build('{input.rmd}')" 2>&1 > {log}
    """

shell:
    """
    R -e "workflowr::wflow_build('{input.rmd}')" 2>&1 > {log}
    """