shell:
    """
    if [ `printf '{input}' | wc -w` -gt 1 ]
    then
        cat {input} > {output}
    else
        ln -sr {input} {output}
    fi

    """

shell:
    """
    fastq_screen --threads {threads} --outdir analysis/fastq_screen/ {input}
    """

shell:
    """
    trim_galore {input} --output_dir analysis/trim_galore/ --cores {threads} --fastqc
    """

shell:
    """
    gatk --java-options "-Xms8g -Xmx{resources.mem_gb}g -Djava.io.tmpdir=./tmp" \
    GenomicsDBImport \
    {params.sample_gvcfs} \
    --genomicsdb-workspace-path {output.genomicsdb} \
    {params.contigs}
    """

shell:
    """
    gatk --java-options "-Xms8g -Xmx{resources.mem_gb}g -Djava.io.tmpdir=./tmp" \
    GenotypeGVCFs \
    -R {params.ref_fasta} \
    -V gendb://{params.genomicsdb} \
    -O {output.vcf}
    """

shell:
    """
    gatk --java-options "-Xms8g -Xmx{resources.mem_gb}g -Djava.io.tmpdir=./tmp" \
    SortVcf \
    -I {input.vcf} \
    -O {output.sorted_vcf} \
    -SD {params.dictionary} 
    """

shell:
    """
    gatk --java-options "-Xms8g -Xmx{resources.mem_gb}g -Djava.io.tmpdir=./tmp" \
    SelectVariants \
    -R {params.ref_fasta} \
    -V {input} \
    --select-type-to-include {wildcards.var_type} \
    -O {output.raw}

    echo "SelectVariants 1 done." >> {log.stdout}
    echo "SelectVariants 1 done." >> {log.stderr}

    gatk --java-options "-Xms8g -Xmx{resources.mem_gb}g -Djava.io.tmpdir=./tmp" \
    VariantFiltration \
    --R {params.ref_fasta} \
    --V {output.raw} \
    {params.filt_params} \
    -O {output.filt} 

    echo "VariantFiltration done." >> {log.stdout}
    echo "VariantFiltration done." >> {log.stderr}

    gatk --java-options "-Xms8g -Xmx{resources.mem_gb}g -Djava.io.tmpdir=./tmp" \
    SelectVariants \
    -R {params.ref_fasta} \
    -V {output.filt} \
    --exclude-filtered \
    -O {output.pass_only} 

    echo "SelectVariants 2 done." >> {log.stdout}
    echo "SelectVariants 2 done." >> {log.stderr}

    vt peek -r {params.ref_fasta} {output.pass_only} 2> {output.vt_peek_pass} 1>>{log.stdout}
    """

shell:
    """
    gatk --java-options "-Xms8g -Xmx{resources.mem_gb}g -Djava.io.tmpdir=./tmp" \
    BaseRecalibrator \
    -R {params.ref_fasta} \
    -I {input.bam} \
    --known-sites {input.known_snps_vcf} \
    --known-sites {input.known_indels_vcf} \
    -O {output.recal_table} 

    echo "BaseRecalibrator done." >> {log.stdout}
    echo "BaseRecalibrator done." >> {log.stderr}

    gatk --java-options "-Xms8g -Xmx{resources.mem_gb}g -Djava.io.tmpdir=./tmp" \
    ApplyBQSR \
    -R {params.ref_fasta} \
    -I {input.bam} \
    -bqsr {output.recal_table} \
    -O {output.recal_bam}

    echo "ApplyBQSR done." >> {log.stdout}
    echo "ApplyBQSR done." >> {log.stderr}

    """